EzCatDB: M00051
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DB codeM00051
RLCP classification3.113.90030.1133 : Transfer
3.1143.90000.1132 : Transfer
CATH domainDomain 13.30.1490.80 : Dna Ligase; domain 1
Domain 23.30.470.20 : D-amino Acid Aminotransferase; Chain A, domain 1Catalytic domain
Domain 31.10.1080.10 : Glutathione Synthetase; Chain A, domain 3Catalytic domain
Domain 43.40.50.1760 : Rossmann fold
Domain 53.30.1490.50 : Dna Ligase; domain 1Catalytic domain
E.C.6.3.2.3
CSA2hgs

CATH domainRelated DB codes (homologues)
3.30.470.20 : D-amino Acid Aminotransferase; Chain A, domain 1T00082,D00298,M00035,M00037,T00107,T00108

Enzyme Name
UniProtKBKEGG

P48637Q08220
Protein nameGlutathione synthetaseGlutathione synthetaseglutathione synthase
glutathione synthetase
GSH synthetase
SynonymsEC 6.3.2.3
Glutathione synthase
GSH synthetase
GSH-S
EC 6.3.2.3
Glutathione synthase
GSH synthetase
GSH-S
RefSeqNP_000169.1 (Protein)
NM_000178.2 (DNA/RNA sequence)
NP_014593.1 (Protein)
NM_001183303.1 (DNA/RNA sequence)
PfamPF03917 (GSH_synth_ATP)
PF03199 (GSH_synthase)
[Graphical view]
PF03917 (GSH_synth_ATP)
PF03199 (GSH_synthase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00251Glutamate metabolism
MAP00480Glutathione metabolism

UniProtKB:Accession NumberP48637Q08220
Entry nameGSHB_HUMANGSHB_YEAST
ActivityATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione.ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione.
SubunitHomodimer (By similarity).
Subcellular location

Cofactor


Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00669C00002C00037C00008C00009C00051
CompoundMagnesiumgamma-L-Glutamyl-L-cysteineATPGlycineADPOrthophosphateGlutathione
Typedivalent metal (Ca2+, Mg2+)amino acids,amide group,sulfhydryl groupamine group,nucleotideamino acidsamine group,nucleotidephosphate group/phosphate ionamino acids,carboxyl group,peptide/protein,sulfhydryl group
ChEBI18420
17515
15422
15428
57305
16761
26078
16856
PubChem888
123938
5957
750
5257127
6022
22486802
1004
25246407
124886
               
2hgsA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0tA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0tB01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0wA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0wB01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hgsA02Bound:_MGUnboundUnboundUnboundUnboundAnalogue:SO4 505Bound:GSH
1m0tA02UnboundUnboundUnboundUnboundUnboundAnalogue:SO4 504Unbound
1m0tB02UnboundUnboundUnboundUnboundUnboundAnalogue:SO4 503Unbound
1m0wA02Bound:_MGAnalogue:3GCAnalogue:ANPUnboundUnboundUnboundUnbound
1m0wB02Bound:_MGAnalogue:3GCAnalogue:ANPUnboundUnboundUnboundUnbound
2hgsA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0tA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0tB03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0wA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0wB03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hgsA04UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0tA04UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0tB04UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0wA04UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0wB04UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hgsA05Bound:_MGUnboundUnboundUnboundBound:ADPUnboundUnbound
1m0tA05UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0tB05UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1m0wA05Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound
1m0wB05Bound:_MGUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [6] & [12]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
2hgsA01 
 
 
 
1m0tA01 
 
 
 
1m0tB01 
 
 
 
1m0wA01 
 
 
 
1m0wB01 
 
 
 
2hgsA02ARG  125;ARG  450
GLU  144(Mg1 & Mg2 binding);ASN  146(Mg2 binding)
SER  151
 
1m0tA02ARG  128;ARG  467
GLU  146(Mg1 & Mg2 binding);ASN  148(Mg2 binding)
SER  153
 
1m0tB02ARG 1128;ARG 1467
GLU 1146(Mg1 & Mg2 binding);ASN 1148(Mg2 binding)
SER 1153
 
1m0wA02ARG  128;ARG  467
GLU  146(Mg1 & Mg2 binding);ASN  148(Mg2 binding)
SER  153
 
1m0wB02ARG 1128;ARG 1467
GLU 1146(Mg1 & Mg2 binding);ASN 1148(Mg2 binding)
SER 1153
 
2hgsA03LYS  305
 
 
 
1m0tA03LYS  324
 
 
 
1m0tB03LYS 1324
 
 
 
1m0wA03LYS  324
 
 
 
1m0wB03LYS 1324
 
 
 
2hgsA04 
 
 
 
1m0tA04 
 
 
 
1m0tB04 
 
 
 
1m0wA04 
 
 
 
1m0wB04 
 
 
 
2hgsA05LYS  364
GLU  368(Mg2 binding)
GLY  369
 
1m0tA05LYS  382
                     
        
invisible 385-388
1m0tB05LYS 1382
                     
        
invisible 1385-1389
1m0wA05LYS  382
GLU  386(Mg2 binding)
GLY  387
 
1m0wB05LYS 1382
GLU 1386(Mg2 binding)
        
invisible 1387-1388

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]p.3208-3209
[12]


references
[1]
PubMed ID447639
JournalJ Biol Chem
Year1979
Volume254
Pages5184-90
AuthorsOppenheimer L, Wellner VP, Griffith OW, Meister A
TitleGlutathione synthetase. Purification from rat kidney and mapping of the substrate binding sites.
[2]
PubMed ID7181863
JournalBiochem J
Year1982
Volume207
Pages65-72
AuthorsYork MJ, Kuchel PW, Chapman BE, Jones AJ
TitleIncorporation of labelled glycine into reduced glutathione of intact human erythrocytes by enzyme-catalysed exchange. A nuclear-magnetic-resonance study.
[3]
PubMed ID6148935
JournalBiomed Biochim Acta
Year1984
Volume43
Pages719-26
AuthorsKuchel PW, Chapman BE, Endre ZH, King GF, Thorburn DR, York MJ
TitleMonitoring metabolic reactions in erythrocytes using NMR spectroscopy.
[4]
PubMed ID7567920
JournalProtein Eng
Year1995
Volume8
Pages353-62
AuthorsMizuguchi K, Go N
TitleComparison of spatial arrangements of secondary structural elements in proteins.
[5]
CommentsHomologous enzyme
PubMed ID9551557
JournalStructure
Year1998
Volume6
Pages363-76
AuthorsLevdikov VM, Barynin VV, Grebenko AI, Melik-Adamyan WR, Lamzin VS, Wilson KS
TitleThe structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis.
[6]
CommentsX-ray crystallography
PubMed ID10369661
JournalEMBO J
Year1999
Volume18
Pages3204-13
AuthorsPolekhina G, Board PG, Gali RR, Rossjohn J, Parker MW
TitleMolecular basis of glutathione synthetase deficiency and a rare gene permutation event.
Related PDB2hgs
[7]
PubMed ID10438618
JournalJ Mol Biol
Year1999
Volume291
Pages239-47
AuthorsGrishin NV
TitlePhosphatidylinositol phosphate kinase: a link between protein kinase and glutathione synthase folds.
[8]
PubMed ID10861239
JournalBiochem J
Year2000
Volume349
Pages275-9
AuthorsNjalsson R, Carlsson K, Olin B, Carlsson B, Whitbread L, Polekhina G, Parker MW, Norgren S, Mannervik B, Board PG, Larsson A
TitleKinetic properties of missense mutations in patients with glutathione synthetase deficiency.
[9]
PubMed ID11964186
JournalBiochem J
Year2002
Volume363
Pages833-8
AuthorsMeierjohann S, Walter RD, Muller S
TitleGlutathione synthetase from Plasmodium falciparum.
[10]
PubMed ID12467574
JournalStructure (Camb)
Year2002
Volume10
Pages1669-76
AuthorsGogos A, Shapiro L
TitleLarge conformational changes in the catalytic cycle of glutathione synthase.
Related PDB1m0t,1m0w
[11]
PubMed ID12734194
JournalJ Biol Chem
Year2003
Volume278
Pages40152-61
AuthorsPhlippen N, Hoffmann K, Fischer R, Wolf K, Zimmermann M
TitleThe glutathione synthetase of Schizosaccharomyces pombe is synthesized as a homodimer but retains full activity when present as a heterotetramer.
[12]
PubMed ID14990577
JournalJ Biol Chem
Year2004
Volume279
Pages22412-21
AuthorsDinescu A, Cundari TR, Bhansali VS, Luo JL, Anderson ME
TitleFunction of conserved residues of human glutathione synthetase: implications for the ATP-grasp enzymes.

comments
According to the literature [6], this enzyme catalyzes two successive transfer reactions. Firstly, it transfers the gamma-phosphate group of ATP to the C-terminal carboxylate of the second substrate, gamma-glutamylcysteine, to form an acylphosphate intermediate. Secondly, it transfers the acyl group from the intermediate to the amine group of the third substrate, glycine, to form a tetrahedral carbon inermediate, which dissociates into the product GSH, releasing inorganic phosphate and ADP.
The first reaction (phosphoryl transfer) proceeds as follows (see [6]):
(1) The acceptor group, the C-terminal carboxylate oxygen of gamma-glutamylcysteine (the first substrate), makes a nucleophilic attack on the transferred group, gamma-phosphate of ATP (the second substrate), leading to the formation of the pentacovalent phosphate transition state.
(2) The mainchain amide of Gly369, and the sidechains of Arg125 and Arg450 stabilize the transferred group, gamma-phosphate, together with two magnesium ions bound to Glu144, Asn146 and Glu368, during the transition state. Meanwhile, Lys305 and Lys364 stabilize the negative charge of the leaving group, alpha- and beta-phosphate groups of ATP (the second substrate), together with the two magnesium ions.
(3) The leaving group, ADP, dissociates, forming an acylphosphate intermediate.
The second reaction (acyl transfer) proceeds as follows (see [6] & [12]):
(1') The acceptor group, the amine of glycine, makes a nucleophilic attack on the transferred group, the carbonyl carbon of the acylphosphate intermediate, forming the tetrahedral intermediate.
(2') The mainchain amide of Ser151, and the sidechain of Arg125 stabilize the charge on the tetrahedral intermediate. Meanwhile, Arg125 and Arg450 stabilize the negative charge of the leaving gamma-phosphate, together with the two magnesium ions.
(3') Finally, the tetrahedral carbon intermediate dissociates to form the product GSH, releasing the inorganic phosphate.

createdupdated
2004-08-012009-03-16


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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