DB code: D00130

RLCP classification 3.133.90030.394 : Transfer
CATH domain 3.40.50.300 : Rossmann fold Catalytic domain
1.10.238.70 : Recoverin; domain 1
E.C. 2.7.4.13
CSA 1dek
M-CSA 1dek
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 D00129 D00540 M00186

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq
P04531 Deoxynucleotide monophosphate kinase
DNK
dNMP kinase
EC 2.7.4.13
Gp1
NP_049752.1 (Protein)
NC_000866.4 (DNA/RNA sequence)

KEGG enzyme name
(deoxy)nucleoside-phosphate kinase
deoxynucleoside monophosphate kinase
deoxyribonucleoside monophosphokinase
deoxynucleoside-5'-monophosphate kinase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P04531 DNMK_BPT4 ATP + deoxynucleoside phosphate = ADP + deoxynucleoside diphosphate. Homodimer.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C03607 C00008 C03786
E.C.
Compound Magnesium ATP Deoxynucleoside phosphate ADP Deoxynucleoside diphosphate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide nucleotide amine group,nucleotide nucleotide
ChEBI 18420
15422
16761
PubChem 888
5957
6022
1dekA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dekB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1delA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1delB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:AMP Unbound Unbound Unbound
1dekA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:DGP Unbound Unbound
1dekB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:DGP Unbound Unbound
1delA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:DGP Unbound Unbound
1delB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:DGP Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [1]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dekA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 10;LYS 14;ARG 177 ASP 15(Magnesium binding)
1dekB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 10;LYS 14;ARG 177 ASP 15(Magnesium binding)
1delA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 10;LYS 14;ARG 177 ASP 15(Magnesium binding)
1delB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 10;LYS 14;ARG 177 ASP 15(Magnesium binding)
1dekA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 68;ARG 132 TYR 42;GLN 85;GLU 108(non-cofactor magnesium binding)
1dekB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 68;ARG 132 TYR 42;GLN 85;GLU 108(non-cofactor magnesium binding)
1delA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 68;ARG 132 TYR 42;GLN 85;GLU 108(non-cofactor magnesium binding)
1delB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 68;ARG 132 TYR 42;GLN 85;GLU 108(non-cofactor magnesium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.3490-3491, p.3493-3495

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID
PubMed ID 8670851
Journal EMBO J
Year 1996
Volume 15
Pages 3487-97
Authors Teplyakov A, Sebastiao P, Obmolova G, Perrakis A, Brush GS, Bessman MJ, Wilson KS
Title Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
Related PDB 1dek 1del
Related UniProtKB P04531
[2]
Resource
Comments
Medline ID
PubMed ID 12597877
Journal Protein Expr Purif
Year 2003
Volume 27
Pages 195-201
Authors Mikoulinskaia GV, Gubanov SI, Zimin AA, Kolesnikov IV, Feofanov SA, Miroshnikov AI
Title Purification and characterization of the deoxynucleoside monophosphate kinase of bacteriophage T5.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 14711503
Journal Protein Expr Purif
Year 2004
Volume 33
Pages 166-75
Authors Mikoulinskaia GV, Zimin AA, Feofanov SA, Miroshnikov AI
Title Identification, cloning, and expression of bacteriophage T5 dnk gene encoding a broad specificity deoxyribonucleoside monophosphate kinase (EC 2.7.4.13).
Related PDB
Related UniProtKB

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.

Created Updated
2004-03-18 2009-02-26