EzCatDB: D00129
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DB codeD00129
RLCP classification3.133.90030.395 : Transfer
CATH domainDomain 13.30.63.10 : Guanylate Kinase phosphate binding domainCatalytic domain
Domain 23.40.50.300 : Rossmann foldCatalytic domain
E.C.2.7.4.8

CATH domainRelated DB codes (homologues)
3.30.63.10 : Guanylate Kinase phosphate binding domainD00540
3.40.50.300 : Rossmann foldS00527,S00547,S00548,S00550,S00554,S00555,S00671,S00672,S00676,S00680,S00682,S00913,S00914,S00301,S00302,S00303,S00304,S00307,S00308,S00305,S00306,S00309,S00310,S00311,M00114,M00199,D00130,D00540,M00186

Enzyme Name
UniProtKBKEGG

P15454Q8I2M1Q64520
Protein nameGuanylate kinase
Guanylate kinaseguanylate kinase
deoxyguanylate kinase
5'-GMP kinase
GMP kinase
guanosine monophosphate kinase
ATP:GMP phosphotransferase
SynonymsEC 2.7.4.8
GMP kinase
Guanylate kinase
EC 2.7.4.8
EC 2.7.4.8
GMP kinase
RefSeqNP_010742.1 (Protein)
NM_001180762.1 (DNA/RNA sequence)
XP_001352159.1 (Protein)
XM_001352123.1 (DNA/RNA sequence)

PfamPF00625 (Guanylate_kin)
[Graphical view]
PF00625 (Guanylate_kin)
[Graphical view]
PF00625 (Guanylate_kin)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism

UniProtKB:Accession NumberP15454Q8I2M1Q64520
Entry nameKGUA_YEASTQ8I2M1_PLAF7KGUA_MOUSE
ActivityATP + GMP = ADP + GDP.
ATP + GMP = ADP + GDP.
SubunitMonomer.
Monomer (By similarity).
Subcellular location


Cofactor



Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00002C00144C00008C00035
CompoundMagnesiumATPGMPADPGDP
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamide group,amine group,nucleotideamine group,nucleotideamide group,amine group,nucleotide
ChEBI18420
15422
17345
16761
17552
PubChem888
5957
6804
6022
8977
             
1ex6A01UnboundUnboundUnboundUnboundUnbound
1ex6B01UnboundUnboundUnboundUnboundUnbound
1ex7A01UnboundUnboundBound:5GPUnboundUnbound
1gkyA01UnboundUnboundBound:5GPUnboundUnbound
1z6gA01UnboundUnboundUnboundUnboundUnbound
1lvgA01UnboundUnboundBound:5GPUnboundUnbound
1ex6A02UnboundUnboundUnboundUnboundUnbound
1ex6B02UnboundUnboundUnboundUnboundUnbound
1ex7A02UnboundUnboundUnboundUnboundUnbound
1gkyA02UnboundUnboundUnboundUnboundUnbound
1z6gA02UnboundUnboundUnboundUnboundUnbound
1lvgA02UnboundUnboundUnboundBound:ADPUnbound

Active-site residues
resource
literature [3], [6] & [9]
pdbCatalytic residuesCofactor-binding residues
          
1ex6A01ARG  38;ARG  41;TYR  50;TYR  78
 
1ex6B01ARG 238;ARG 241;TYR 250;TYR 278
 
1ex7A01ARG  38;ARG  41;TYR  50;TYR  78
 
1gkyA01ARG  38;ARG  41;TYR  50;TYR  78
 
1z6gA01ARG  41;ARG  44;TYR  53;TYR  81
 
1lvgA01ARG  41;ARG  44;TYR  53;TYR  81
 
1ex6A02LYS  14;ARG 135;ARG 146
ASP  98(Magnesium binding)
1ex6B02LYS 214;ARG 335;ARG 346
ASP 298(Magnesium binding)
1ex7A02LYS  14;ARG 135;ARG 146
ASP  98(Magnesium binding)
1gkyA02LYS  14;ARG 135;ARG 146
ASP  98(Magnesium binding)
1z6gA02LYS  17;ARG 139;ARG 150
GLU 101(Magnesium binding)
1lvgA02LYS  17;ARG 137;ARG 148
ASP 101(Magnesium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.1140
[6]p.110-119
[9]p.30241

references
[1]
PubMed ID2551688
JournalEur J Biochem
Year1989
Volume184
Pages433-43
AuthorsBerger A, Schiltz E, Schulz GE
TitleGuanylate kinase from Saccharomyces cerevisiae. Isolation and characterization, crystallization and preliminary X-ray analysis, amino acid sequence and comparison with adenylate kinases.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID90133954
PubMed ID1967656
JournalJ Mol Biol
Year1990
Volume211
Pages249-54
AuthorsStehle T, Schulz GE
TitleThree-dimensional structure of the complex of guanylate kinase from yeast with its substrate GMP.
Related UniProtKBP15454
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID92235848
PubMed ID1314905
JournalJ Mol Biol
Year1992
Volume224
Pages1127-41
AuthorsStehle T, Schulz GE
TitleRefined structure of the complex between guanylate kinase and its substrate GMP at 2.0 A resolution.
Related PDB1gky
Related UniProtKBP15454
[4]
PubMed ID8910414
JournalJ Biol Chem
Year1996
Volume271
Pages28038-44
AuthorsLi Y, Zhang Y, Yan H
TitleKinetic and thermodynamic characterizations of yeast guanylate kinase.
[5]
PubMed ID9235932
JournalJ Biol Chem
Year1997
Volume272
Pages19343-50
AuthorsZhang Y, Li Y, Wu Y, Yan H
TitleStructural and functional roles of tyrosine 78 of yeast guanylate kinase.
[6]
PubMed ID10218107
JournalAdv Enzymol Relat Areas Mol Biol
Year1999
Volume73
Pages103-34
AuthorsYan H, Tsai MD
TitleNucleoside monophosphate kinases: structure, mechanism, and substrate specificity.
[7]
PubMed ID10939525
JournalMol Biol Rep
Year2000
Volume27
Pages45-9
AuthorsKumar V
TitleCloning and sequence analysis of lily and tobacco guanylate kinases.
[8]
CommentsX-ray crystallography
PubMed ID11243817
JournalJ Mol Biol
Year2001
Volume307
Pages247-57
AuthorsBlaszczyk J, Li Y, Yan H, Ji X
TitleCrystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes.
Related PDB1ex6,1ex7
[9]
PubMed ID12036965
JournalJ Biol Chem
Year2002
Volume277
Pages30236-43
AuthorsSekulic N, Shuvalova L, Spangenberg O, Konrad M, Lavie A
TitleStructural characterization of the closed conformation of mouse guanylate kinase.
Related PDB1lvg

comments
This enzyme is homologous to the counterpart enzyme from bacteria (D00540 in EzCatDB).
Although the catalytic mechanism of this enzyme must be similar to that of adenylate kinase (S00305 in EzCatDB), according to the literature [3] & [6], the catalytic residues are a little bit different.
Along with basic residues (Lys14, Arg38, Arg41, Arg135 & Arg146 of 1ex7), tyrosine residues (Tyr50 & Tyr78) act as stabilizers for the transition state.
Although magnesium bound structures have not been reported for this enzyme, Asp98 must play a role in binding of magnesium ion.
Moreover, the literature [6] supported the associative mechanism (or SN2 mechanism).

createdupdated
2004-03-182009-04-08
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)
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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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