3.6.4.B7: RadA recombinase
This is an abbreviated version!
For detailed information about RadA recombinase, go to the full flat file.
Word Map on EC 3.6.4.B7
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3.6.4.B7
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strand
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brca2
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single-stranded
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meiotic
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fork
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checkpoint
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reca
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ssdna
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nucleoprotein
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helicase
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stall
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radiosensitivity
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non-homologous
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dna-damaging
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fanconi
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radiation-induced
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chromatid
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mre11
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h2ax
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interstrand
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end-joining
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recombinases
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chk1
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meiosis-specific
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homology-directed
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olaparib
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dna-pkcs
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fancd2
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restart
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prophase
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synaptonemal
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parpis
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error-free
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reca-like
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unrepaired
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gamma-h2ax
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dsb-induced
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d-loops
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ctip
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break-induced
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translesion
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holliday
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bard1
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molecular biology
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synthesis
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atr-dependent
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topbp1
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ssdna-binding
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brca1-mutant
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rucaparib
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diagnostics
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analysis
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pharmacology
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xrcc4
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brca1-deficient
- 3.6.4.B7
- strand
- brca2
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single-stranded
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meiotic
- fork
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checkpoint
- reca
- ssdna
- nucleoprotein
- helicase
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stall
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radiosensitivity
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non-homologous
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dna-damaging
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fanconi
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radiation-induced
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chromatid
- mre11
- h2ax
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interstrand
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end-joining
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recombinases
- chk1
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meiosis-specific
-
homology-directed
- olaparib
- dna-pkcs
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fancd2
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restart
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prophase
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synaptonemal
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parpis
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error-free
-
reca-like
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unrepaired
-
gamma-h2ax
-
dsb-induced
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d-loops
- ctip
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break-induced
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translesion
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holliday
- bard1
- molecular biology
- synthesis
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atr-dependent
-
topbp1
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ssdna-binding
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brca1-mutant
- rucaparib
- diagnostics
- analysis
- pharmacology
- xrcc4
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brca1-deficient
Reaction
Synonyms
DNA repair and recombination protein, DNA repair protein RAD51 homolog 1, Hvo RadA, MvRadA, Pho RadA, PhoRadA, Rad51, RadA, RadA intein, RadA recombinase, RadA/Sms, RadC1, RadC2, SMS, SSO0250, SsoRadA, SsoRadA recombinase, SsRada
ECTree
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General Information
General Information on EC 3.6.4.B7 - RadA recombinase
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evolution
malfunction
metabolism
physiological function
additional information
cis-splicing of the engineered RadAmin intein is very efficient and indistinguishable from that of PhoRadA intein, suggesting that the removed disordered loop is a mere remnant from the endonuclease domain that was lost during evolution
evolution
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the enzyme belongs to the RecA/RadA family of recombinase proteins of the AAA + ATPases, including RecA proteins of bacteria, RadAs in archaea, Rad51 and DMC1 proteins in Eukaryotes. Archaea and eukaryotes encode RadA/Rad51 paralogues, such as Rad55/57 in yeast, Rad51B/C/D, Xrcc2 and Xrcc3 in mammals, and RadB, RadC in Archaea, which facilitate homologous recombination by interacting with RadA/Rad51 recombinases. Archaeal RadA and eukaryotic Rad51 proteins show high amino acid sequence identities to each other (over 40%) but they are more distantly related to bacterial RecA proteins, exhibiting about 20% sequence identity. Archaeal and eukaryotic recombinases are also more closely related to each other at protein domain structure. RadA paralogues represent another major group of AAA + ATPases involved in DNA damage repair in Archaea
evolution
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the enzyme belongs to the RecA/RadA family of recombinase proteins of the AAA + ATPases, including RecA proteins of bacteria, RadAs in archaea, Rad51 and DMC1 proteins in Eukaryotes. Archaea and eukaryotes encode RadA/Rad51 paralogues, such as Rad55/57 in yeast, Rad51B/C/D, Xrcc2 and Xrcc3 in mammals, and RadB, RadC in Archaea, which facilitate homologous recombination by interacting with RadA/Rad51 recombinases. Archaeal RadA and eukaryotic Rad51 proteins show high amino acid sequence identities to each other (over 40%) but they are more distantly related to bacterial RecA proteins, exhibiting about 20% sequence identity. Archaeal and eukaryotic recombinases are also more closely related to each other at protein domain structure. RadA paralogues represent another major group of AAA + ATPases involved in DNA damage repair in Archaea
evolution
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the enzyme belongs to the RecA/RadA family of recombinase proteins of the AAA + ATPases, including RecA proteins of bacteria, RadAs in archaea, Rad51 and DMC1 proteins in Eukaryotes. Archaea and eukaryotes encode RadA/Rad51 paralogues, such as Rad55/57 in yeast, Rad51B/C/D, Xrcc2 and Xrcc3 in mammals, and RadB, RadC in Archaea, which facilitate homologous recombination by interacting with RadA/Rad51 recombinases. Archaeal RadA and eukaryotic Rad51 proteins show high amino acid sequence identities to each other (over 40%) but they are more distantly related to bacterial RecA proteins, exhibiting about 20% sequence identity. Archaeal and eukaryotic recombinases are also more closely related to each other at protein domain structure. RadA paralogues represent another major group of AAA + ATPases involved in DNA damage repair in Archaea
evolution
the enzyme belongs to the RecA/RadA family of recombinase proteins of the AAA + ATPases, including RecA proteins of bacteria, RadAs in archaea, Rad51 and DMC1 proteins in Eukaryotes. Archaea and eukaryotes encode RadA/Rad51 paralogues, such as Rad55/57 in yeast, Rad51B/C/D, Xrcc2 and Xrcc3 in mammals, and RadB, RadC in Archaea, which facilitate homologous recombination by interacting with RadA/Rad51 recombinases. Archaeal RadA and eukaryotic Rad51 proteins show high amino acid sequence identities to each other (over 40%) but they are more distantly related to bacterial RecA proteins, exhibiting about 20% sequence identity. Archaeal and eukaryotic recombinases are also more closely related to each other at protein domain structure. RadA paralogues represent another major group of AAA + ATPases involved in DNA damage repair in Archaea
evolution
the enzyme belongs to the RecA/RadA family of recombinase proteins of the AAA + ATPases, including RecA proteins of bacteria, RadAs in archaea, Rad51 and DMC1 proteins in Eukaryotes. Archaea and eukaryotes encode RadA/Rad51 paralogues, such as Rad55/57 in yeast, Rad51B/C/D, Xrcc2 and Xrcc3 in mammals, and RadB, RadC in Archaea, which facilitate homologous recombination by interacting with RadA/Rad51 recombinases. Archaeal RadA and eukaryotic Rad51 proteins show high amino acid sequence identities to each other (over 40%) but they are more distantly related to bacterial RecA proteins, exhibiting about 20% sequence identity. Archaeal and eukaryotic recombinases are also more closely related to each other at protein domain structure. RadA paralogues represent another major group of AAA + ATPases involved in DNA damage repair in Archaea
evolution
the enzyme belongs to the RecA/RadA family of recombinase proteins, including RecA proteins of bacteria, RadAs in archaea, Rad51 and DMC1 proteins in Eukaryotes. Archaea and eukaryotes encode RadA/Rad51 paralogues, such as Rad55/57 in yeast, Rad51B/C/D, Xrcc2 and Xrcc3 in mammals, and RadB, RadC in Archaea, which facilitate homologous recombination by interacting with RadA/Rad51 recombinases. Archaeal RadA and eukaryotic Rad51 proteins show high amino acid sequence identities to each other (over 40%) but they are more distantly related to bacterial RecA proteins, exhibiting about 20% sequence identity. Archaeal and eukaryotic recombinases are also more closely related to each other at protein domain structure. RadA paralogues represent another major group of AAA + ATPases involved in DNA damage repair in Archaea
evolution
the enzyme belongs to the RecA/RadA family of recombinase proteins, including RecA proteins of bacteria, RadAs in archaea, Rad51 and DMC1 proteins in Eukaryotes. Archaea and eukaryotes encode RadA/Rad51 paralogues, such as Rad55/57 in yeast, Rad51B/C/D, Xrcc2 and Xrcc3 in mammals, and RadB, RadC in Archaea, which facilitate homologous recombination by interacting with RadA/Rad51 recombinases. Archaeal RadA and eukaryotic Rad51 proteins show high amino acid sequence identities to each other (over 40%) but they are more distantly related to bacterial RecA proteins, exhibiting about 20% sequence identity. Archaeal and eukaryotic recombinases are also more closely related to each other at protein domain structure. RadA paralogues represent another major group of AAA + ATPases involved in DNA damage repair in Archaea
evolution
Bacillus subtilis encodes three branch migration translocases: RuvAB, RecG, and RadA, i.e. Sms
evolution
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the enzyme belongs to the RecA/RadA family of recombinase proteins of the AAA + ATPases, including RecA proteins of bacteria, RadAs in archaea, Rad51 and DMC1 proteins in Eukaryotes. Archaea and eukaryotes encode RadA/Rad51 paralogues, such as Rad55/57 in yeast, Rad51B/C/D, Xrcc2 and Xrcc3 in mammals, and RadB, RadC in Archaea, which facilitate homologous recombination by interacting with RadA/Rad51 recombinases. Archaeal RadA and eukaryotic Rad51 proteins show high amino acid sequence identities to each other (over 40%) but they are more distantly related to bacterial RecA proteins, exhibiting about 20% sequence identity. Archaeal and eukaryotic recombinases are also more closely related to each other at protein domain structure. RadA paralogues represent another major group of AAA + ATPases involved in DNA damage repair in Archaea
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evolution
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Bacillus subtilis encodes three branch migration translocases: RuvAB, RecG, and RadA, i.e. Sms
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evolution
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cis-splicing of the engineered RadAmin intein is very efficient and indistinguishable from that of PhoRadA intein, suggesting that the removed disordered loop is a mere remnant from the endonuclease domain that was lost during evolution
-
evolution
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the enzyme belongs to the RecA/RadA family of recombinase proteins of the AAA + ATPases, including RecA proteins of bacteria, RadAs in archaea, Rad51 and DMC1 proteins in Eukaryotes. Archaea and eukaryotes encode RadA/Rad51 paralogues, such as Rad55/57 in yeast, Rad51B/C/D, Xrcc2 and Xrcc3 in mammals, and RadB, RadC in Archaea, which facilitate homologous recombination by interacting with RadA/Rad51 recombinases. Archaeal RadA and eukaryotic Rad51 proteins show high amino acid sequence identities to each other (over 40%) but they are more distantly related to bacterial RecA proteins, exhibiting about 20% sequence identity. Archaeal and eukaryotic recombinases are also more closely related to each other at protein domain structure. RadA paralogues represent another major group of AAA + ATPases involved in DNA damage repair in Archaea
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a null radA mutation impairs chromosomal transformation, in the absence of RadA competent cells require the RecG translocase for natural chromosomal transformation. A RadA/SmsC4 mutation impairs chromosomal and plasmid transformation. Enzyme mutants RadA C13A or C13R fail to interact with RecA and do not promote unwinding of a non-cognate 3'-tailed or 5'-fork DNA substrate. Enzyme mutants RadA C13A and C13R hydrolyse ATP in a ssDNA-dependent manner. Mutant RadA C13A interacts with itself but does not interact with RecA. RadA C13A and C13R variants preferentially bind ssDNA, albeit with lower efficiency than the wild-type enzyme. RadA C13A and C13R mutants bind natural ssDNA and partially displace SsbA
malfunction
loss of radA, by itself, reduces recovery of genetic rearrangements at tandem-repeated sequences, which are promoted by defects in the replication fork helicase, DnaB. In addition, loss of RadA reduces homologous recombination when in combination with loss of RuvAB or RecG as measured by conjugation with Hfr donors (RuvAB and RecG are DNA motor proteins that branch-migrate recombination intermediates such as Holliday junctions during the late stages of homologous recombination). Mutations in the Walker A, KNRFG and zinc finger motifs abolish RadA's branch migration activity in RecA-coupled reactions and lead to the accumulation of strand exchange intermediate species
malfunction
translocase depletion in tumor cell lines leads to the accumulation of RAD51 on chromosomes, forming complexes that are not associated with markers of DNA damage. Combined depletion of RAD54L and RAD54B and/or artificial induction of RAD51 overexpression blocks replication and promotes chromosome segregation defects. Induction of nondamage-associated RAD51 foci is associated with reduced cell growth. Replication defects and mitotic defects associated with accumulation of nondamage-associated RAD51 complexes, overview
malfunction
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a null radA mutation impairs chromosomal transformation, in the absence of RadA competent cells require the RecG translocase for natural chromosomal transformation. A RadA/SmsC4 mutation impairs chromosomal and plasmid transformation. Enzyme mutants RadA C13A or C13R fail to interact with RecA and do not promote unwinding of a non-cognate 3'-tailed or 5'-fork DNA substrate. Enzyme mutants RadA C13A and C13R hydrolyse ATP in a ssDNA-dependent manner. Mutant RadA C13A interacts with itself but does not interact with RecA. RadA C13A and C13R variants preferentially bind ssDNA, albeit with lower efficiency than the wild-type enzyme. RadA C13A and C13R mutants bind natural ssDNA and partially displace SsbA
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nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. The proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Some are active during DNA damage repair. All nanobiomotors contain an ATPase domain that adopts RecA fold structure, characteristic for RecA/RadA family proteins, structural analyses of archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion
metabolism
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nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. The proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Some are active during DNA damage repair. All nanobiomotors contain an ATPase domain that adopts RecA fold structure, characteristic for RecA/RadA family proteins, structural analyses of archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion
metabolism
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nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. The proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Some are active during DNA damage repair. All nanobiomotors contain an ATPase domain that adopts RecA fold structure, characteristic for RecA/RadA family proteins, structural analyses of archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion
metabolism
nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. The proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Some are active during DNA damage repair. All nanobiomotors contain an ATPase domain that adopts RecA fold structure, characteristic for RecA/RadA family proteins, structural analyses of archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion
metabolism
nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. The proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Some are active during DNA damage repair. All nanobiomotors contain an ATPase domain that adopts RecA fold structure, characteristic for RecA/RadA family proteins, structural analyses of archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion
metabolism
nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. The proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Some are active during DNA damage repair. All nanobiomotors contain an ATPase domain that adopts RecA fold structure, characteristic for RecA/RadA family proteins, structural analyses of archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion
metabolism
nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. The proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Some are active during DNA damage repair. All nanobiomotors contain an ATPase domain that adopts RecA fold structure, characteristic for RecA/RadA family proteins, structural analyses of archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion
metabolism
RAD54 family translocases prevent accumulation of nondamage-associated RAD51 complexes in MCF-7 cells
metabolism
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nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. The proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Some are active during DNA damage repair. All nanobiomotors contain an ATPase domain that adopts RecA fold structure, characteristic for RecA/RadA family proteins, structural analyses of archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion
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metabolism
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nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. The proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Some are active during DNA damage repair. All nanobiomotors contain an ATPase domain that adopts RecA fold structure, characteristic for RecA/RadA family proteins, structural analyses of archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion
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archaeal RadA proteins are close homologues of eukaryal Rad51 and DMC1 proteins and are remote homologues of bacterial RecA proteins. For the repair of double-stranded breaks in DNA, these recombinases promote a pivotal strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. This DNA-repair function also plays a key role in the resistance of cancer cells to chemotherapy and radiotherapy and in the resistance of bacterial cells to antibiotics
physiological function
homologous recombinational repair is an essential mechanism for repair of double-strand breaks in DNA. Recombinases of the RecA-fold family play a crucial role in this process, forming filaments that utilize ATP to mediate their interactions with singleand double-stranded DNA
physiological function
play a key role in DNA repair by forming helical nucleoprotein filaments which promote a hallmark strand exchange reaction between homologous DNA substrates
physiological function
RecA family protein filaments may function as rotary motors
physiological function
recombinases of the RecA family play vital roles in homologous recombination, a high-fidelity mechanism to repair DNA double-stranded breaks. These proteins catalyze strand invasion and exchange after forming dynamic nucleoprotein filaments on ssDNA
physiological function
the enzyme is involved in homologous recombination
physiological function
the enzyme promotes recombination at temperatures approaching the DNA melting point
physiological function
homologous recombination protein RadA/Rad51 recombinase binds to 3'-pertruding ends of dsDNA mediating the strand invasion reaction in homologous recombination. The recombinases are essential mediators of homologous recombination, an activity that is required for repairing dsDNA breaks and re-starting of stalled DNA replication forks. The RecA/RadA-facilitated strand exchange reaction occurs in two steps: (a) the recombinases bind to ssDNA, forming a nucleoprotein complex, and (b) the nucleoprotein complex invades a homologous dsDNA, such that the invading RadA-ssDNA base pairs with the complimentary strand of the dsDNA whereas the other stranded of the DNA becomes ssDNA, forming a so-called D-loop structure. The D-loop structure is a very important intermediate in DNA repair or DNA replication processes. Rotation mechanism of the enzyme nanobiomotor
physiological function
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homologous recombination protein RadA/Rad51 recombinase binds to 3'-pertruding ends of dsDNA mediating the strand invasion reaction in homologous recombination. The recombinases are essential mediators of homologous recombination, an activity that is required for repairing dsDNA breaks and re-starting of stalled DNA replication forks. The RecA/RadA-facilitated strand exchange reaction occurs in two steps: (a) the recombinases bind to ssDNA, forming a nucleoprotein complex, and (b) the nucleoprotein complex invades a homologous dsDNA, such that the invading RadA-ssDNA base pairs with the complimentary strand of the dsDNA whereas the other stranded of the DNA becomes ssDNA, forming a so-called D-loop structure. The D-loop structure is a very important intermediate in DNA repair or DNA replication processes. Rotation mechanism of the enzyme nanobiomotor. RadA provides a prototype nanobiomotor for studying conversion of chemical energy to mechanical movement. In the clockwise rotation model, ATP binding and hydrolysis at the core domain result in repositioning of NTD and core domain and rotation between two adjacent subunits. Unlike most nanobiomotors that translocate along DNA, RadA polymers do not move along ssDNA or dsDNA but rotate around the axis like F1 ATPase
physiological function
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homologous recombination protein RadA/Rad51 recombinase binds to 3'-pertruding ends of dsDNA mediating the strand invasion reaction in homologous recombination. The recombinases are essential mediators of homologous recombination, an activity that is required for repairing dsDNA breaks and re-starting of stalled DNA replication forks. The RecA/RadA-facilitated strand exchange reaction occurs in two steps: (a) the recombinases bind to ssDNA, forming a nucleoprotein complex, and (b) the nucleoprotein complex invades a homologous dsDNA, such that the invading RadA-ssDNA base pairs with the complimentary strand of the dsDNA whereas the other stranded of the DNA becomes ssDNA, forming a so-called D-loop structure. The D-loop structure is a very important intermediate in DNA repair or DNA replication processes. Rotation mechanism of the enzyme nanobiomotor. RadA provides a prototype nanobiomotor for studying conversion of chemical energy to mechanical movement. In the clockwise rotation model, ATP binding and hydrolysis at the core domain result in repositioning of NTD and core domain and rotation between two adjacent subunits. Unlike most nanobiomotors that translocate along DNA, RadA polymers do not move along ssDNA or dsDNA but rotate around the axis like F1 ATPase
physiological function
homologous recombination protein RadA/Rad51 recombinase binds to 3'-pertruding ends of dsDNA mediating the strand invasion reaction in homologous recombination. The recombinases are essential mediators of homologous recombination, an activity that is required for repairing dsDNA breaks and re-starting of stalled DNA replication forks. The RecA/RadA-facilitated strand exchange reaction occurs in two steps: (a) the recombinases bind to ssDNA, forming a nucleoprotein complex, and (b) the nucleoprotein complex invades a homologous dsDNA, such that the invading RadA-ssDNA base pairs with the complimentary strand of the dsDNA whereas the other stranded of the DNA becomes ssDNA, forming a so-called D-loop structure. The D-loop structure is a very important intermediate in DNA repair or DNA replication processes. Rotation mechanism of the enzyme nanobiomotor. RadA provides a prototype nanobiomotor for studying conversion of chemical energy to mechanical movement. In the clockwise rotation model, ATP binding and hydrolysis at the core domain result in repositioning of NTD and core domain and rotation between two adjacent subunits. Unlike most nanobiomotors that translocate along DNA, RadA polymers do not move along ssDNA or dsDNA but rotate around the axis like F1 ATPase
physiological function
homologous recombination protein RadA/Rad51 recombinase binds to 3'-pertruding ends of dsDNA mediating the strand invasion reaction in homologous recombination. The recombinases are essential mediators of homologous recombination, an activity that is required for repairing dsDNA breaks and re-starting of stalled DNA replication forks. The RecA/RadA-facilitated strand exchange reaction occurs in two steps: (a) the recombinases bind to ssDNA, forming a nucleoprotein complex, and (b) the nucleoprotein complex invades a homologous dsDNA, such that the invading RadA-ssDNA base pairs with the complimentary strand of the dsDNA whereas the other stranded of the DNA becomes ssDNA, forming a so-called D-loop structure. The D-loop structure is a very important intermediate in DNA repair or DNA replication processes. Rotation mechanism of the enzyme nanobiomotor. RadA provides a prototype nanobiomotor for studying conversion of chemical energy to mechanical movement. In the clockwise rotation model, ATP binding and hydrolysis at the core domain result in repositioning of NTD and core domain and rotation between two adjacent subunits. Unlike most nanobiomotors that translocate along DNA, RadA polymers do not move along ssDNA or dsDNA but rotate around the axis like F1 ATPase
physiological function
homologous recombination protein RadA/Rad51 recombinase binds to 3'-pertruding ends of dsDNA mediating the strand invasion reaction in homologous recombination. The recombinases are essential mediators of homologous recombination, an activity that is required for repairing dsDNA breaks and re-starting of stalled DNA replication forks. The RecA/RadA-facilitated strand exchange reaction occurs in two steps: (a) the recombinases bind to ssDNA, forming a nucleoprotein complex, and (b) the nucleoprotein complex invades a homologous dsDNA, such that the invading RadA-ssDNA base pairs with the complimentary strand of the dsDNA whereas the other stranded of the DNA becomes ssDNA, forming a so-called D-loop structure. The D-loop structure is a very important intermediate in DNA repair or DNA replication processes. Rotation mechanism of the enzyme nanobiomotor. RadA provides a prototype nanobiomotor for studying conversion of chemical energy to mechanical movement. In the clockwise rotation model, ATP binding and hydrolysis at the core domain result in repositioning of NTD and core domain and rotation between two adjacent subunits. Unlike most nanobiomotors that translocate along DNA, RadA polymers do not move along ssDNA or dsDNA but rotate around the axis like F1 ATPase
physiological function
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homologous recombination protein RadA/Rad51 recombinase binds to 3'-pertruding ends of dsDNA mediating the strand invasion reaction in homologous recombination. The recombinases are essentialmediators of homologous recombination, an activity that is required for repairing dsDNA breaks and re-starting of stalled DNA replication forks. The RecA/RadA-facilitated strand exchange reaction occurs in two steps: (a) the recombinases bind to ssDNA, forming a nucleoprotein complex, and (b) the nucleoprotein complex invades a homologous dsDNA, such that the invading RadA-ssDNA base pairs with the complimentary strand of the dsDNA whereas the other stranded of the DNA becomes ssDNA, forming a so-called D-loop structure. The D-loop structure is a very important intermediate in DNA repair or DNA replication processes. Rotation mechanism of the enzyme nanobiomotor. RadA provides a prototype nanobiomotor for studying conversion of chemical energy to mechanical movement. In the clockwise rotation model, ATP binding and hydrolysis at the core domain result in repositioning of NTD and core domain and rotation between two adjacent subunits. Unlike most nanobiomotors that translocate along DNA, RadA polymers do not move along ssDNA or dsDNA but rotate around the axis like F1 ATPase
physiological function
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the archaeon may not encode a eukarya-type of NER (nucleotide excision repair) pathway because depleting each of the eukaryal NER homologues XPD, XPB and XPF does not impair the DNA repair capacity in their mutants. But among seven homologous recombination proteins, including RadA, Hel308/Hjm, Rad50, Mre11, HerA, NurA and Hjc, only the Hjc nuclease is dispensable for cell viability. Analysis of genetic mechanisms of DNA repair in this model organism, overview
physiological function
RadA can bind to single-stranded DNA and stimulate branch migration to increase the rate of homologous recombination. RadA allows branch migration to occur even when RecA is missing, but RadA is unable to begin strand exchange if RecA is not present. The process of branch migration stabilizes the DNA molecules during homologous recombination and may also allow the repaired DNA strand to engage the machinery that copies DNA. In vitro RecA mediates strand exchange, a key step of recombination. RadA has an effect on the structure of RecA. The wild-type RadA protein preferentially binds single-strand DNA in the presence of ADP, exhibits ATPase activity stimulated by DNA, and increases the rate of RecA-mediated recombination in vitro by stimulation of branch migration. Branch migration can be mediated by RadA even in the absence of RecA and is highly directional in nature, with preferential extension of the heteroduplex in the 5' to 3' direction, relative to the initiating single-strand, this is codirectional with that of RecA-mediated strand exchange. DNA branch migration and exchange mechanism, overview
physiological function
the strand exchange protein RAD51 functions to promote genome stability by repairing DNA double strand breaks (DSB) and damaged replication forks. RAD51 repairs damage by forming helical nucleoprotein filaments on tracts of ssDNA. Such tracts form by 5'-3' processing of DNA ends formed by DSBs, and also as a consequence of replication fork collapse or blockage. The ssDNA-specific binding protein RPA binds rapidly and with high specificity to ssDNA tracts and, with the help of mediator proteins, promotes the recruitment of RAD51. Following nucleoprotein filament formation, RAD51 carries out a search for homologous dsDNA sequences and then promotes invasion of target duplex leading to the exchange of DNA strands that forms heteroduplex DNA within an intermediate called the displacement loop (D-loop). The ssDNA strand displaced from the target duplex during heteroduplex DNA formation also binds RPA. Subsequent stages of the recombination process result in repair of damage without loss or rearrangement of DNA sequences. RAD54L and RAD54B counteract genome-destabilizing effects of direct binding of RAD51 to dsDNA in human tumor cells. Thus, in addition to having genome-stabilizing DNA repair activity, human RAD51 has genome-destabilizing activity when expressed at high levels, as is the case in many human tumors. Within the RPA-positive subpopulation, induction of RAD51 overexpression was associated with redistribution of RPA from the diffuse staining pattern to punctate foci, suggesting that they form on undamage dsDNA, with subsequent local accumulation of RPA foci as a consequence of replisome collisions with preformed RAD51 fibers
physiological function
wild-type RadA interacts with and inhibits the ATPase activity of RecA (BG214). RadA and its mutant variants, C13A and C13R, bound to the 5'-tail of a DNA substrate, unwind DNA in the 5'->3' direction. RecA interacts with and loads wild-type RadA to promote unwinding of a non-cognate 3'-tailed or 5'-fork DNA substrate. Wild-type RadA interaction with RecA is crucial to recruit the former onto D-loop DNA, and both proteins in concert catalyse D-loop extension to favour integration of ssDNA during chromosomal transformation. But RadA inhibits the ATPase activity of RecA. Proposed model for the action of the 5'->3' RadA helicase in coordination with RecA during natural transformation and in double strand break repair, overview. RadA is crucial for chromosomal transformation, but is essential in the DELTArecG background. Functional analysis, detailed overview
physiological function
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recombinases of the RecA family play vital roles in homologous recombination, a high-fidelity mechanism to repair DNA double-stranded breaks. These proteins catalyze strand invasion and exchange after forming dynamic nucleoprotein filaments on ssDNA
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physiological function
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homologous recombinational repair is an essential mechanism for repair of double-strand breaks in DNA. Recombinases of the RecA-fold family play a crucial role in this process, forming filaments that utilize ATP to mediate their interactions with singleand double-stranded DNA
-
physiological function
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RecA family protein filaments may function as rotary motors
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physiological function
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homologous recombination protein RadA/Rad51 recombinase binds to 3'-pertruding ends of dsDNA mediating the strand invasion reaction in homologous recombination. The recombinases are essential mediators of homologous recombination, an activity that is required for repairing dsDNA breaks and re-starting of stalled DNA replication forks. The RecA/RadA-facilitated strand exchange reaction occurs in two steps: (a) the recombinases bind to ssDNA, forming a nucleoprotein complex, and (b) the nucleoprotein complex invades a homologous dsDNA, such that the invading RadA-ssDNA base pairs with the complimentary strand of the dsDNA whereas the other stranded of the DNA becomes ssDNA, forming a so-called D-loop structure. The D-loop structure is a very important intermediate in DNA repair or DNA replication processes. Rotation mechanism of the enzyme nanobiomotor. RadA provides a prototype nanobiomotor for studying conversion of chemical energy to mechanical movement. In the clockwise rotation model, ATP binding and hydrolysis at the core domain result in repositioning of NTD and core domain and rotation between two adjacent subunits. Unlike most nanobiomotors that translocate along DNA, RadA polymers do not move along ssDNA or dsDNA but rotate around the axis like F1 ATPase
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physiological function
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wild-type RadA interacts with and inhibits the ATPase activity of RecA (BG214). RadA and its mutant variants, C13A and C13R, bound to the 5'-tail of a DNA substrate, unwind DNA in the 5'->3' direction. RecA interacts with and loads wild-type RadA to promote unwinding of a non-cognate 3'-tailed or 5'-fork DNA substrate. Wild-type RadA interaction with RecA is crucial to recruit the former onto D-loop DNA, and both proteins in concert catalyse D-loop extension to favour integration of ssDNA during chromosomal transformation. But RadA inhibits the ATPase activity of RecA. Proposed model for the action of the 5'->3' RadA helicase in coordination with RecA during natural transformation and in double strand break repair, overview. RadA is crucial for chromosomal transformation, but is essential in the DELTArecG background. Functional analysis, detailed overview
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physiological function
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homologous recombination protein RadA/Rad51 recombinase binds to 3'-pertruding ends of dsDNA mediating the strand invasion reaction in homologous recombination. The recombinases are essential mediators of homologous recombination, an activity that is required for repairing dsDNA breaks and re-starting of stalled DNA replication forks. The RecA/RadA-facilitated strand exchange reaction occurs in two steps: (a) the recombinases bind to ssDNA, forming a nucleoprotein complex, and (b) the nucleoprotein complex invades a homologous dsDNA, such that the invading RadA-ssDNA base pairs with the complimentary strand of the dsDNA whereas the other stranded of the DNA becomes ssDNA, forming a so-called D-loop structure. The D-loop structure is a very important intermediate in DNA repair or DNA replication processes. Rotation mechanism of the enzyme nanobiomotor
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catalytic site structure analysis, the scissile peptide bond between Met-1 and Ala1 of minimized RadA intein is in the usual transconformation
additional information
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catalytic site structure analysis, the scissile peptide bond between Met-1 and Ala1 of minimized RadA intein is in the usual transconformation
additional information
determination of structures of one of inteins with high splicing efficiency, the RadA intein from Pyrococcus horikoshii (PhoRadA). The solution NMR structure and the crystal structures elucidate the structural basis for its high efficiency, precise interactions between N-extein and the intein, NMR structure determination and structure-function analysis, overview. Comparison between the NMR and crystal structures of PhoRadA intein
additional information
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determination of structures of one of inteins with high splicing efficiency, the RadA intein from Pyrococcus horikoshii (PhoRadA). The solution NMR structure and the crystal structures elucidate the structural basis for its high efficiency, precise interactions between N-extein and the intein, NMR structure determination and structure-function analysis, overview. Comparison between the NMR and crystal structures of PhoRadA intein
additional information
Sulfolobus tokodaii encodes four putative RadA paralogues, RadA paralogue stRadC2 is involved in DNA recombination via interaction with recombinase RadA and the Holliday junction Hjc. stRadC2 inhibits the strand exchange activity of RadA and facilitates Hjc-mediated Holliday junction DNA cleavage in vitro. stRadC2 may act as an anti-recombination factor in DNA recombinational repair in Sulfolobus tokodaii
additional information
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Sulfolobus tokodaii encodes four putative RadA paralogues, RadA paralogue stRadC2 is involved in DNA recombination via interaction with recombinase RadA and the Holliday junction Hjc. stRadC2 inhibits the strand exchange activity of RadA and facilitates Hjc-mediated Holliday junction DNA cleavage in vitro. stRadC2 may act as an anti-recombination factor in DNA recombinational repair in Sulfolobus tokodaii
additional information
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the ring and right-handed filament structures of RadAs, domain structure and organization, overview. In the absence of ATP, the Walker motifs adopt a conformation to hold the ATP-binding site open and do not interact with the adjacent ATPase domain
additional information
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the ring and right-handed filament structures of RadAs, domain structure and organization, overview. In the absence of ATP, the Walker motifs adopt a conformation to hold the ATP-binding site open and do not interact with the adjacent ATPase domain
additional information
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the ring and right-handed filament structures of RadAs, domain structure and organization, overview. In the absence of ATP, the Walker motifs adopt a conformation to hold the ATP-binding site open and do not interact with the adjacent ATPase domain
additional information
the ring and right-handed filament structures of RadAs, domain structure and organization, overview. In the absence of ATP, the Walker motifs adopt a conformation to hold the ATP-binding site open and do not interact with the adjacent ATPase domain
additional information
the ring and right-handed filament structures of RadAs, domain structure and organization, overview. In the absence of ATP, the Walker motifs adopt a conformation to hold the ATP-binding site open and do not interact with the adjacent ATPase domain
additional information
the ring and right-handed filament structures of RadAs, domain structure and organization, overview. In the absence of ATP, the Walker motifs adopt a conformation to hold the ATP-binding site open and do not interact with the adjacent ATPase domain
additional information
the ring and right-handed filament structures of RadAs, domain structure and organization, overview. In the absence of ATP, the Walker motifs adopt a conformation to hold the ATP-binding site open and do not interact with the adjacent ATPase domain
additional information
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comparisons of nucleotide-bound enzyme and enzyme mutant structure, overview. Nucleotide binding might have an allosteric and/or co-operative effect on the binding to FxxA sequences and plays an additional role in regulating the oligomeric structures of the recombinase
additional information
comparisons of nucleotide-bound enzyme and enzyme mutant structure, overview. Nucleotide binding might have an allosteric and/or co-operative effect on the binding to FxxA sequences and plays an additional role in regulating the oligomeric structures of the recombinase
additional information
homology modeling of the Hvo RadA primary sequence using the Pfu RadA structure (PDB ID 1PZN) chain A as the highest scoring template. Consistent with its function as a recombinase, ATP and DNA binding motifs are apparent which have a well-conserved sequence composition despite the common skews in overall amino acid usage typically observed in halophilic proteins
additional information
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homology modeling of the Hvo RadA primary sequence using the Pfu RadA structure (PDB ID 1PZN) chain A as the highest scoring template. Consistent with its function as a recombinase, ATP and DNA binding motifs are apparent which have a well-conserved sequence composition despite the common skews in overall amino acid usage typically observed in halophilic proteins
additional information
RAD51 fibers may be helical nucleoprotein filaments
additional information
RadA is a 460 amino acid protein that has three well-conserved domains also found in other proteins, as well as a 5-amino acid motif highly conserved among radA orthologs. The N-terminal 30 amino acids form a putative zinc-finger domain with a C4 motif, CXXC-Xn-CXXC
additional information
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RadA is a 460 amino acid protein that has three well-conserved domains also found in other proteins, as well as a 5-amino acid motif highly conserved among radA orthologs. The N-terminal 30 amino acids form a putative zinc-finger domain with a C4 motif, CXXC-Xn-CXXC
additional information
splicing of RadA intein located in the ATPase domain of the hyperthermophilic archaeon Pyrococcus horikoshii is strongly regulated by the native exteins, which lock the intein in an inactive state. This splicing trap occurs through interactions between distant residues in the native exteins and the intein, in three-dimensional space. The exteins might thereby serve as an environmental sensor, releasing the intein for full activity only at optimal growth conditions for the native organism, while sparing ATP consumption under conditions of cold-shock. This partnership between the intein and its exteins, which implies coevolution of the parasitic intein and its host protein may provide another means of post-translational control. Homology models for the RadA extein and intein are generated separately based on the closest templates for the extein: PDB ID 2ZUB, and for the intein: PDB ID 4E2T, molecular dynamics simulations, overview. The catalytic residues of the intein are located on the extein-intein interface, revealing the possibility for 3D extein-intein interactions affecting intein catalysis. Conserved residues of the intein C153, H245, H312, H323 and N324 are oriented toward the RadA exteins
additional information
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splicing of RadA intein located in the ATPase domain of the hyperthermophilic archaeon Pyrococcus horikoshii is strongly regulated by the native exteins, which lock the intein in an inactive state. This splicing trap occurs through interactions between distant residues in the native exteins and the intein, in three-dimensional space. The exteins might thereby serve as an environmental sensor, releasing the intein for full activity only at optimal growth conditions for the native organism, while sparing ATP consumption under conditions of cold-shock. This partnership between the intein and its exteins, which implies coevolution of the parasitic intein and its host protein may provide another means of post-translational control. Homology models for the RadA extein and intein are generated separately based on the closest templates for the extein: PDB ID 2ZUB, and for the intein: PDB ID 4E2T, molecular dynamics simulations, overview. The catalytic residues of the intein are located on the extein-intein interface, revealing the possibility for 3D extein-intein interactions affecting intein catalysis. Conserved residues of the intein C153, H245, H312, H323 and N324 are oriented toward the RadA exteins
additional information
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homology modeling of the Hvo RadA primary sequence using the Pfu RadA structure (PDB ID 1PZN) chain A as the highest scoring template. Consistent with its function as a recombinase, ATP and DNA binding motifs are apparent which have a well-conserved sequence composition despite the common skews in overall amino acid usage typically observed in halophilic proteins
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additional information
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the ring and right-handed filament structures of RadAs, domain structure and organization, overview. In the absence of ATP, the Walker motifs adopt a conformation to hold the ATP-binding site open and do not interact with the adjacent ATPase domain
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additional information
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comparisons of nucleotide-bound enzyme and enzyme mutant structure, overview. Nucleotide binding might have an allosteric and/or co-operative effect on the binding to FxxA sequences and plays an additional role in regulating the oligomeric structures of the recombinase
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additional information
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homology modeling of the Hvo RadA primary sequence using the Pfu RadA structure (PDB ID 1PZN) chain A as the highest scoring template. Consistent with its function as a recombinase, ATP and DNA binding motifs are apparent which have a well-conserved sequence composition despite the common skews in overall amino acid usage typically observed in halophilic proteins
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additional information
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comparisons of nucleotide-bound enzyme and enzyme mutant structure, overview. Nucleotide binding might have an allosteric and/or co-operative effect on the binding to FxxA sequences and plays an additional role in regulating the oligomeric structures of the recombinase
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additional information
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comparisons of nucleotide-bound enzyme and enzyme mutant structure, overview. Nucleotide binding might have an allosteric and/or co-operative effect on the binding to FxxA sequences and plays an additional role in regulating the oligomeric structures of the recombinase
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additional information
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homology modeling of the Hvo RadA primary sequence using the Pfu RadA structure (PDB ID 1PZN) chain A as the highest scoring template. Consistent with its function as a recombinase, ATP and DNA binding motifs are apparent which have a well-conserved sequence composition despite the common skews in overall amino acid usage typically observed in halophilic proteins
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additional information
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comparisons of nucleotide-bound enzyme and enzyme mutant structure, overview. Nucleotide binding might have an allosteric and/or co-operative effect on the binding to FxxA sequences and plays an additional role in regulating the oligomeric structures of the recombinase
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additional information
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catalytic site structure analysis, the scissile peptide bond between Met-1 and Ala1 of minimized RadA intein is in the usual transconformation
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additional information
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determination of structures of one of inteins with high splicing efficiency, the RadA intein from Pyrococcus horikoshii (PhoRadA). The solution NMR structure and the crystal structures elucidate the structural basis for its high efficiency, precise interactions between N-extein and the intein, NMR structure determination and structure-function analysis, overview. Comparison between the NMR and crystal structures of PhoRadA intein
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additional information
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the ring and right-handed filament structures of RadAs, domain structure and organization, overview. In the absence of ATP, the Walker motifs adopt a conformation to hold the ATP-binding site open and do not interact with the adjacent ATPase domain
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additional information
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homology modeling of the Hvo RadA primary sequence using the Pfu RadA structure (PDB ID 1PZN) chain A as the highest scoring template. Consistent with its function as a recombinase, ATP and DNA binding motifs are apparent which have a well-conserved sequence composition despite the common skews in overall amino acid usage typically observed in halophilic proteins
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additional information
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comparisons of nucleotide-bound enzyme and enzyme mutant structure, overview. Nucleotide binding might have an allosteric and/or co-operative effect on the binding to FxxA sequences and plays an additional role in regulating the oligomeric structures of the recombinase
-
additional information
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splicing of RadA intein located in the ATPase domain of the hyperthermophilic archaeon Pyrococcus horikoshii is strongly regulated by the native exteins, which lock the intein in an inactive state. This splicing trap occurs through interactions between distant residues in the native exteins and the intein, in three-dimensional space. The exteins might thereby serve as an environmental sensor, releasing the intein for full activity only at optimal growth conditions for the native organism, while sparing ATP consumption under conditions of cold-shock. This partnership between the intein and its exteins, which implies coevolution of the parasitic intein and its host protein may provide another means of post-translational control. Homology models for the RadA extein and intein are generated separately based on the closest templates for the extein: PDB ID 2ZUB, and for the intein: PDB ID 4E2T, molecular dynamics simulations, overview. The catalytic residues of the intein are located on the extein-intein interface, revealing the possibility for 3D extein-intein interactions affecting intein catalysis. Conserved residues of the intein C153, H245, H312, H323 and N324 are oriented toward the RadA exteins
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additional information
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homology modeling of the Hvo RadA primary sequence using the Pfu RadA structure (PDB ID 1PZN) chain A as the highest scoring template. Consistent with its function as a recombinase, ATP and DNA binding motifs are apparent which have a well-conserved sequence composition despite the common skews in overall amino acid usage typically observed in halophilic proteins
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additional information
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homology modeling of the Hvo RadA primary sequence using the Pfu RadA structure (PDB ID 1PZN) chain A as the highest scoring template. Consistent with its function as a recombinase, ATP and DNA binding motifs are apparent which have a well-conserved sequence composition despite the common skews in overall amino acid usage typically observed in halophilic proteins
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additional information
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homology modeling of the Hvo RadA primary sequence using the Pfu RadA structure (PDB ID 1PZN) chain A as the highest scoring template. Consistent with its function as a recombinase, ATP and DNA binding motifs are apparent which have a well-conserved sequence composition despite the common skews in overall amino acid usage typically observed in halophilic proteins
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