EzCatDB: D00130

DB codeD00130
RLCP classification3.133.90030.394
CATH domainDomain 13.40.50.300Catalytic domain
Domain 21.10.238.70
E.C.2.7.4.13
CSA1dek

CATH domainRelated DB codes (homologues)
3.40.50.300S00527,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,D00129,D00540,M00186

Enzyme Name
Swiss-protKEGG

P04531
Protein nameDeoxynucleotide monophosphate kinase(deoxy)nucleoside-phosphate kinase
deoxynucleoside monophosphate kinase
deoxyribonucleoside monophosphokinase
deoxynucleoside-5'-monophosphate kinase
SynonymsdNMP kinase
DNK
EC 2.7.4.13
Gp1


Swiss-prot:Accession NumberP04531
Entry nameDNMK_BPT4
ActivityATP + deoxynucleoside phosphate = ADP + deoxynucleoside diphosphate.
SubunitHomodimer.
Subcellular location
Cofactor


CofactorsSubstratesProducts
KEGG-idC00305C00002C03607C00008C03786
CompoundMagnesiumATPDeoxynucleoside phosphateADPDeoxynucleoside diphosphate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidenucleotideamine group,nucleotidenucleotide
1dekA01UnboundUnboundUnboundUnboundUnbound
1dekB01UnboundUnboundUnboundUnboundUnbound
1delA01UnboundUnboundUnboundUnboundUnbound
1delB01UnboundAnalogue:AMPUnboundUnboundUnbound
1dekA02UnboundUnboundBound:DGPUnboundUnbound
1dekB02UnboundUnboundBound:DGPUnboundUnbound
1delA02UnboundUnboundBound:DGPUnboundUnbound
1delB02UnboundUnboundBound:DGPUnboundUnbound

Active-site residues
resource
literature [1]
pdbCatalytic residuesCofactor-binding residues
1dekA01LYS  10;LYS  14;ARG 177
ASP  15(Magnesium binding)
1dekB01LYS  10;LYS  14;ARG 177
ASP  15(Magnesium binding)
1delA01LYS  10;LYS  14;ARG 177
ASP  15(Magnesium binding)
1delB01LYS  10;LYS  14;ARG 177
ASP  15(Magnesium binding)
1dekA02ARG  68;ARG 132
TYR  42;GLN  85;GLU 108(non-cofactor magnesium binding)
1dekB02ARG  68;ARG 132
TYR  42;GLN  85;GLU 108(non-cofactor magnesium binding)
1delA02ARG  68;ARG 132
TYR  42;GLN  85;GLU 108(non-cofactor magnesium binding)
1delB02ARG  68;ARG 132
TYR  42;GLN  85;GLU 108(non-cofactor magnesium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.3490-3491, p.3493-3495

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
PubMed ID8670851
JournalEMBO J
Year1996
Volume15
Pages3487-97
AuthorsTeplyakov A, Sebastiao P, Obmolova G, Perrakis A, Brush GS, Bessman MJ, Wilson KS
TitleCrystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
Related PDB1dek,1del
Related Swiss-protP04531
[2]
PubMed ID12597877
JournalProtein Expr Purif
Year2003
Volume27
Pages195-201
AuthorsMikoulinskaia GV, Gubanov SI, Zimin AA, Kolesnikov IV, Feofanov SA, Miroshnikov AI
TitlePurification and characterization of the deoxynucleoside monophosphate kinase of bacteriophage T5.
[3]
PubMed ID14711503
JournalProtein Expr Purif
Year2004
Volume33
Pages166-75
AuthorsMikoulinskaia GV, Zimin AA, Feofanov SA, Miroshnikov AI
TitleIdentification, cloning, and expression of bacteriophage T5 dnk gene encoding a broad specificity deoxyribonucleoside monophosphate kinase (EC 2.7.4.13).

comments
This enzyme is composed of two domains, NTP-binding domain and NMP-binding domain.
Although the second domain of this enzyme binds a magnesium ion, it is not involved in catalysis. Instead, it may stabilize the domain strucure (see [1]). Thus, it is not a cofactor. However, this enzyme probably requires a catalytic magnesium ion as a cofactor, which may be bound to Asp15 (see [1]). The literature [1] mentioned that the binding site for the cofactor magnesium must be formed only after the triphosphate of NTP is bound to the enzyme.
According to the literature [1], this enzyme may have a similar catalytic mechanism to that of adenylate kinases (S00305 in EzCatDB).
Divalent cations must activate a nucleophile (gamma-phosphate group of substrate NTP), and stabilize the transition state (see [1]). The negative charge of the transferred phosphoryl group and acceptor phosphoryl group must be stabilized by Lysine/Alginine cluster.

createdupdated
2004-03-182009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
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 2010)
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)

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