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show all sequences of 2.5.1.73

Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus

Fukunaga, R.; Yokoyama, S.; J. Mol. Biol. 370, 128-141 (2007)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
SepCysS1, overexpression in Escherichia coli strain BL21(DE3), expression of selenomethionine-labeled SepCysS1 in Escherichia coli strain B834
Archaeoglobus fulgidus
Crystallization (Commentary)
Crystallization
Organism
purified recombinant wild-type SepVysS1 and selenomethionine-labeled SepCysS1, hanging-drop vapor diffusion method, 0.001 ml protein solution is mixed with 0.001 ml reservoir solution containing 80 mM sodium acetate buffer, pH 4.4, 160 mM NaCl, and 1.00 M ammonium sulfate, 20C, equilibration against 0.5 ml reservoir solution, cryoprotection by 25% v/v glycerol, X-ray diffraction structure determination and analysis at 2.4-3.2 A resolution, modeling
Archaeoglobus fulgidus
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
sulfate
is bound in the proximity of PLP by the side-chains of the conserved Arg79, His103, and Tyr104 residues, the PLP-bound active site is located deep within the large, basic cleft for recognizing Sep-tRNACys
Archaeoglobus fulgidus
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
additional information
Archaeoglobus fulgidus
two-step Cys-tRNACys formation: in organisms like Archaeoglobus fulgidus lacking a canonical cysteinyl-tRNA synthetase for the direct Cys-tRNACys formation, Cys-tRNACys is produced by the indirect pathway, in which the non-canonical O-phosphoseryl-tRNA synthetase, SepRS, ligates the non-canonical amino acid O-phosphoserine, Sep, to tRNACys, and the Sep-tRNA:Cys-tRNA synthase converts the produced Sep-tRNACys to Cys-tRNACys, overview, the SepRS/SepCysS pathway is the sole route for cysteine biosynthesis in the organism
?
-
-
-
O-phospho-L-seryl-tRNACys + sulfate
Archaeoglobus fulgidus
the in vivo sulfur donor is not determined
L-cysteinyl-tRNACys + phosphate
-
-
-
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Archaeoglobus fulgidus
O30207
SepCysS1; SepCysS1
-
Purification (Commentary)
Commentary
Organism
recombinant SepCysS1 from Escherichia coli strain BL21(DE3) by anion exchange chromatography and affinity chromatography on a heparin resin, recombinant selenomethionine-labeled SepCysS1 from Escherichia coli strain B834
Archaeoglobus fulgidus
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
two-step Cys-tRNACys formation: in organisms like Archaeoglobus fulgidus lacking a canonical cysteinyl-tRNA synthetase for the direct Cys-tRNACys formation, Cys-tRNACys is produced by the indirect pathway, in which the non-canonical O-phosphoseryl-tRNA synthetase, SepRS, ligates the non-canonical amino acid O-phosphoserine, Sep, to tRNACys, and the Sep-tRNA:Cys-tRNA synthase converts the produced Sep-tRNACys to Cys-tRNACys, overview, the SepRS/SepCysS pathway is the sole route for cysteine biosynthesis in the organism
675447
Archaeoglobus fulgidus
?
-
-
-
-
additional information
the active site contains an internal aldimine Lys209-PLP and the sulfate ion, SepCysS should not bind Sep-tRNASec and discriminate tRNACys from tRNASec on the basis of the differences in the length of the T-arms, or SepCysS recognizes the discriminator sequence, which is Ura73 in tRNACys and Gua73 in tRNASec, overview
675447
Archaeoglobus fulgidus
?
-
-
-
-
O-phospho-L-seryl-tRNACys + sulfate
the in vivo sulfur donor is not determined
675447
Archaeoglobus fulgidus
L-cysteinyl-tRNACys + phosphate
-
-
-
-
O-phospho-L-seryl-tRNACys + sulfide
modeling of tRNA binding, overview, sulfide, persulfide, and thiosulfate, but not cysteine, can function as sulfur donor in vitro, the active site is located deep within the large, basic cleft to accommodate Sep-tRNACys, binding modeling of Sep-tRNACys, overview, possibly the side-chain of a Cys residue in SepCysS becomes persulfided as a sulfur transfer intermediate state
675447
Archaeoglobus fulgidus
L-cysteinyl-tRNACys + phosphate
-
-
-
-
Subunits
Subunits
Commentary
Organism
dimer
the active site is located near the dimer interface, crystal structure analysis, overview
Archaeoglobus fulgidus
More
amino acid residue conservation mapping on the basis of the surface electrostatic potential, overview, construction of a SepRS-tRNACys-SepCysS ternary complex model, in the ternary complex the phosphoserylated 3'-terminus of tRNACys can possibly be transferred directly from SepRS to SepCysS, for conversion to the cysteinylated form, overview
Archaeoglobus fulgidus
Cofactor
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
dependent on, pyridoxal 5'-phosphate is covalently bound to the side-chain of the conserved Lys209 at the active site
Archaeoglobus fulgidus
Cloned(Commentary) (protein specific)
Commentary
Organism
SepCysS1, overexpression in Escherichia coli strain BL21(DE3), expression of selenomethionine-labeled SepCysS1 in Escherichia coli strain B834
Archaeoglobus fulgidus
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
dependent on, pyridoxal 5'-phosphate is covalently bound to the side-chain of the conserved Lys209 at the active site
Archaeoglobus fulgidus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant wild-type SepVysS1 and selenomethionine-labeled SepCysS1, hanging-drop vapor diffusion method, 0.001 ml protein solution is mixed with 0.001 ml reservoir solution containing 80 mM sodium acetate buffer, pH 4.4, 160 mM NaCl, and 1.00 M ammonium sulfate, 20C, equilibration against 0.5 ml reservoir solution, cryoprotection by 25% v/v glycerol, X-ray diffraction structure determination and analysis at 2.4-3.2 A resolution, modeling
Archaeoglobus fulgidus
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
sulfate
is bound in the proximity of PLP by the side-chains of the conserved Arg79, His103, and Tyr104 residues, the PLP-bound active site is located deep within the large, basic cleft for recognizing Sep-tRNACys
Archaeoglobus fulgidus
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
additional information
Archaeoglobus fulgidus
two-step Cys-tRNACys formation: in organisms like Archaeoglobus fulgidus lacking a canonical cysteinyl-tRNA synthetase for the direct Cys-tRNACys formation, Cys-tRNACys is produced by the indirect pathway, in which the non-canonical O-phosphoseryl-tRNA synthetase, SepRS, ligates the non-canonical amino acid O-phosphoserine, Sep, to tRNACys, and the Sep-tRNA:Cys-tRNA synthase converts the produced Sep-tRNACys to Cys-tRNACys, overview, the SepRS/SepCysS pathway is the sole route for cysteine biosynthesis in the organism
?
-
-
-
O-phospho-L-seryl-tRNACys + sulfate
Archaeoglobus fulgidus
the in vivo sulfur donor is not determined
L-cysteinyl-tRNACys + phosphate
-
-
-
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant SepCysS1 from Escherichia coli strain BL21(DE3) by anion exchange chromatography and affinity chromatography on a heparin resin, recombinant selenomethionine-labeled SepCysS1 from Escherichia coli strain B834
Archaeoglobus fulgidus
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
two-step Cys-tRNACys formation: in organisms like Archaeoglobus fulgidus lacking a canonical cysteinyl-tRNA synthetase for the direct Cys-tRNACys formation, Cys-tRNACys is produced by the indirect pathway, in which the non-canonical O-phosphoseryl-tRNA synthetase, SepRS, ligates the non-canonical amino acid O-phosphoserine, Sep, to tRNACys, and the Sep-tRNA:Cys-tRNA synthase converts the produced Sep-tRNACys to Cys-tRNACys, overview, the SepRS/SepCysS pathway is the sole route for cysteine biosynthesis in the organism
675447
Archaeoglobus fulgidus
?
-
-
-
-
additional information
the active site contains an internal aldimine Lys209-PLP and the sulfate ion, SepCysS should not bind Sep-tRNASec and discriminate tRNACys from tRNASec on the basis of the differences in the length of the T-arms, or SepCysS recognizes the discriminator sequence, which is Ura73 in tRNACys and Gua73 in tRNASec, overview
675447
Archaeoglobus fulgidus
?
-
-
-
-
O-phospho-L-seryl-tRNACys + sulfate
the in vivo sulfur donor is not determined
675447
Archaeoglobus fulgidus
L-cysteinyl-tRNACys + phosphate
-
-
-
-
O-phospho-L-seryl-tRNACys + sulfide
modeling of tRNA binding, overview, sulfide, persulfide, and thiosulfate, but not cysteine, can function as sulfur donor in vitro, the active site is located deep within the large, basic cleft to accommodate Sep-tRNACys, binding modeling of Sep-tRNACys, overview, possibly the side-chain of a Cys residue in SepCysS becomes persulfided as a sulfur transfer intermediate state
675447
Archaeoglobus fulgidus
L-cysteinyl-tRNACys + phosphate
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
the active site is located near the dimer interface, crystal structure analysis, overview
Archaeoglobus fulgidus
More
amino acid residue conservation mapping on the basis of the surface electrostatic potential, overview, construction of a SepRS-tRNACys-SepCysS ternary complex model, in the ternary complex the phosphoserylated 3'-terminus of tRNACys can possibly be transferred directly from SepRS to SepCysS, for conversion to the cysteinylated form, overview
Archaeoglobus fulgidus
Other publictions for EC 2.5.1.73
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
728697
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19
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3
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19
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1
1
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722261
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2
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2
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539-553
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1
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1
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5
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4
1
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2
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3
2
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1
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4
1
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687743
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Methanosarcina mazei
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283
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2008
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1
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3
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4
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1
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1
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3
1
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1
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2
2
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3
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2
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1
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3
1
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689145
Zhang
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Methanocaldococcus jannaschii
Nat. Struct. Mol. Biol.
15
507-514
2008
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1
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1
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3
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1
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3
1
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1
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1
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1
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3
1
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-
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-
-
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-
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675447
Fukunaga
Structural insights into the s ...
Archaeoglobus fulgidus
J. Mol. Biol.
370
128-141
2007
-
-
1
1
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-
-
-
-
1
-
2
-
3
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1
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4
2
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1
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1
1
1
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1
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2
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1
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4
2
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676784
O'Donoghue
The evolutionary history of Cy ...
Archaeoglobus fulgidus, Methanococcoides burtonii, Methanopyrus kandleri, Methanospirillum hungatei
Proc. Natl. Acad. Sci. USA
102
19003-19008
2005
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4
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4
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4
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8
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4
4
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8
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677118
Sauerwald
RNA-dependent cysteine biosynt ...
Methanocaldococcus jannaschii, Methanococcus maripaludis
Science
307
1969-1972
2005
-
-
1
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1
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2
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5
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1
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