DB code: D00129

RLCP classification 3.133.90030.395 : Transfer
CATH domain 3.30.63.10 : Guanylate Kinase phosphate binding domain Catalytic domain
3.40.50.300 : Rossmann fold Catalytic domain
E.C. 2.7.4.8
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.300 : Rossmann fold S00527 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
3.30.63.10 : Guanylate Kinase phosphate binding domain D00540

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P15454 Guanylate kinase
EC 2.7.4.8
GMP kinase
NP_010742.1 (Protein)
NM_001180762.1 (DNA/RNA sequence)
PF00625 (Guanylate_kin)
[Graphical View]
Q8I2M1
Guanylate kinase
EC 2.7.4.8
XP_001352159.1 (Protein)
XM_001352123.1 (DNA/RNA sequence)
PF00625 (Guanylate_kin)
[Graphical View]
Q64520 Guanylate kinase
EC 2.7.4.8
GMP kinase
PF00625 (Guanylate_kin)
[Graphical View]

KEGG enzyme name
guanylate kinase
deoxyguanylate kinase
5'-GMP kinase
GMP kinase
guanosine monophosphate kinase
ATP:GMP phosphotransferase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P15454 KGUA_YEAST ATP + GMP = ADP + GDP. Monomer.
Q8I2M1 Q8I2M1_PLAF7
Q64520 KGUA_MOUSE ATP + GMP = ADP + GDP. Monomer (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00144 C00008 C00035
E.C.
Compound Magnesium ATP GMP ADP GDP
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amide group,amine group,nucleotide amine group,nucleotide amide group,amine group,nucleotide
ChEBI 18420
15422
17345
16761
17552
PubChem 888
5957
6804
6022
8977
1ex6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ex6B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ex7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:5GP Unbound Unbound
1gkyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:5GP Unbound Unbound
1z6gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1lvgA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:5GP Unbound Unbound
1ex6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ex6B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ex7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gkyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1z6gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1lvgA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ADP Unbound

Reference for Active-site residues
resource references E.C.
literature [3], [6] & [9]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ex6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 38;ARG 41;TYR 50;TYR 78
1ex6B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 238;ARG 241;TYR 250;TYR 278
1ex7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 38;ARG 41;TYR 50;TYR 78
1gkyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 38;ARG 41;TYR 50;TYR 78
1z6gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 41;ARG 44;TYR 53;TYR 81
1lvgA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 41;ARG 44;TYR 53;TYR 81
1ex6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 14;ARG 135;ARG 146 ASP 98(Magnesium binding)
1ex6B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 214;ARG 335;ARG 346 ASP 298(Magnesium binding)
1ex7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 14;ARG 135;ARG 146 ASP 98(Magnesium binding)
1gkyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 14;ARG 135;ARG 146 ASP 98(Magnesium binding)
1z6gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 17;ARG 139;ARG 150 GLU 101(Magnesium binding)
1lvgA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 17;ARG 137;ARG 148 ASP 101(Magnesium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.1140
[6]
p.110-119
[9]
p.30241

References
[1]
Resource
Comments
Medline ID
PubMed ID 2551688
Journal Eur J Biochem
Year 1989
Volume 184
Pages 433-43
Authors Berger A, Schiltz E, Schulz GE
Title Guanylate kinase from Saccharomyces cerevisiae. Isolation and characterization, crystallization and preliminary X-ray analysis, amino acid sequence and comparison with adenylate kinases.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 90133954
PubMed ID 1967656
Journal J Mol Biol
Year 1990
Volume 211
Pages 249-54
Authors Stehle T, Schulz GE
Title Three-dimensional structure of the complex of guanylate kinase from yeast with its substrate GMP.
Related PDB
Related UniProtKB P15454
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 92235848
PubMed ID 1314905
Journal J Mol Biol
Year 1992
Volume 224
Pages 1127-41
Authors Stehle T, Schulz GE
Title Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 A resolution.
Related PDB 1gky
Related UniProtKB P15454
[4]
Resource
Comments
Medline ID
PubMed ID 8910414
Journal J Biol Chem
Year 1996
Volume 271
Pages 28038-44
Authors Li Y, Zhang Y, Yan H
Title Kinetic and thermodynamic characterizations of yeast guanylate kinase.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9235932
Journal J Biol Chem
Year 1997
Volume 272
Pages 19343-50
Authors Zhang Y, Li Y, Wu Y, Yan H
Title Structural and functional roles of tyrosine 78 of yeast guanylate kinase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 10218107
Journal Adv Enzymol Relat Areas Mol Biol
Year 1999
Volume 73
Pages 103-34
Authors Yan H, Tsai MD
Title Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10939525
Journal Mol Biol Rep
Year 2000
Volume 27
Pages 45-9
Authors Kumar V
Title Cloning and sequence analysis of lily and tobacco guanylate kinases.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11243817
Journal J Mol Biol
Year 2001
Volume 307
Pages 247-57
Authors Blaszczyk J, Li Y, Yan H, Ji X
Title Crystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes.
Related PDB 1ex6 1ex7
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12036965
Journal J Biol Chem
Year 2002
Volume 277
Pages 30236-43
Authors Sekulic N, Shuvalova L, Spangenberg O, Konrad M, Lavie A
Title Structural characterization of the closed conformation of mouse guanylate kinase.
Related PDB 1lvg
Related UniProtKB

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).

Created Updated
2004-03-18 2009-04-08