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Information on EC 3.6.4.B7 - RadA recombinase

for references in articles please use BRENDA:EC3.6.4.B7
preliminary BRENDA-supplied EC number
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UNIPROT: O73948
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Word Map
The expected taxonomic range for this enzyme is: Archaea, Bacteria, Eukaryota
Reaction Schemes
Synonyms
rad51, rada/sms, ssorada, rada recombinase, rada intein, dna repair protein rad51 homolog 1, radc1, dna repair and recombination protein, mvrada, hvo rada, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + H2O
ADP + phosphate
show the reaction diagram
additional information
?
-
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. Formation of RadA-ssDNA filaments and stabilization, rotation mechanism of the enzyme nanobiomotor, overview
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + H2O
ADP + phosphate
show the reaction diagram
-
-
-
?
additional information
?
-
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. Formation of RadA-ssDNA filaments and stabilization, rotation mechanism of the enzyme nanobiomotor, overview
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
Mg2+ als well as K+ ions are absorbed at the ATPase center. K+ (but not Na+), stimulates the ATP hydrolysis reaction with an apparent dissociation constant of about 40 mM. The strand exchange activity of the wild-type enzyme is also stimulated by potassium with an apparent dissociation constant of 35 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NaCl
minimal inhibitory effect by 40 mM NaCl further suggests that the protein does not have adequate affinity for sodium
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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
physiological function
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
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
RADA_METVO
322
0
35189
Swiss-Prot
-
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
enzyme domain organization, structure comparisons, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis, enzyme with bound AMP-PNP, PDB ID 1T4G
crystallization of a hexameric form of a truncated Methanococcus voltae RadA protein devoid of its small N-terminal domain, crystals are grown by the hanging drop method The RadA hexamers further assemble into two-ringed assemblies
hanging drop crystallization method at 21 °C. Enzyme in complex with AMP-PNP and K+ (2.7 A resolution), enzyme in complex with AMP-PNP (2.9 A resolution), enzyme in complex with ADP (2.4 A resolution)
hanging drop crystallization method at 21°C crystal structure of the enzyme in complex with ADP and Mg2+ at 2.1 A resolution
hanging drop crystallization method at room temperature, enzyme in complex with the ATP analog AMP-PNP at 2.0 A resolution. The RadA filament is a 106.7 A pitch helix with six subunits per turn. The DNA binding loops L1 and L2 are located in close proximity to the filament axis. The ATP analog is buried between two RadA subunits
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D246A
loss of binding a second Mg2+. Initial ATP turnover rate is reduced by about 20-fold
D246N
initial ATP turnover rate is reduced by about 20-fold
D302K
mutant protein shows comparable strand exchange efficiencies in the presence of either potassium or sodium
E151D
mutant protein retains potassium preference in promoting strand exchange. Reduced ATPase activity and normal strand exchange activity
E151K
mutant protein retains potassium preference in promoting strand exchange. Reduced ATPase activity and normal strand exchange activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pharmacology
application potential of archaeal nanobiomotors in drug delivery
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Du, L.; Luo, Y.
Structure of a hexameric form of RadA recombinase from Methanococcus voltae
Acta Crystallogr. Sect. F
68
511-516
2012
Methanococcus voltae (O73948), Methanococcus voltae
Manually annotated by BRENDA team
Qian, X.; Wu, Y.; He, Y.; Luo, Y.
Crystal structure of Methanococcus voltae RadA in complex with ADP: hydrolysis-induced conformational change
Biochemistry
44
13753-13761
2005
Methanococcus voltae (O73948), Methanococcus voltae
Manually annotated by BRENDA team
Qian, X.; He, Y.; Luo, Y.
Binding of a second magnesium is required for ATPase activity of RadA from Methanococcus voltae
Biochemistry
46
5855-5863
2007
Methanococcus voltae (O73948), Methanococcus voltae
Manually annotated by BRENDA team
Qian, X.; He, Y.; Wu, Y.; Luo, Y.
Asp302 determines potassium dependence of a RadA recombinase from Methanococcus voltae
J. Mol. Biol.
360
537-547
2006
Methanococcus voltae (O73948), Methanococcus voltae
Manually annotated by BRENDA team
Wu, Y.; He, Y.; Moya, I.A.; Qian, X.; Luo, Y.
Crystal structure of archaeal recombinase RADA: a snapshot of its extended conformation
Mol. Cell.
15
423-435
2004
Methanococcus voltae (O73948), Methanococcus voltae
Manually annotated by BRENDA team
Han, W.; Shen, Y.; She, Q.
Nanobiomotors of archaeal DNA repair machineries: current research status and application potential
Cell Biosci.
4
32
2014
Archaeoglobus fulgidus, Sulfolobus islandicus, Sulfurisphaera tokodaii, Methanococcus voltae (O73948), Pyrococcus furiosus (O74036), Saccharolobus solfataricus (Q55075), Thermoplasma acidophilum (Q9HJ68), Saccharolobus solfataricus P2 (Q55075), Thermoplasma acidophilum ATCC 25905 (Q9HJ68)
Manually annotated by BRENDA team