DB code: D00130

RLCP classification	3.133.90030.394 : Transfer
CATH domain	3.40.50.300 : Rossmann fold	Catalytic domain
CATH 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 18420	15422 15422		16761 16761
PubChem	888 888	5957 5957		6022 6022

1dekA01	Unbound	Unbound	Unbound	Unbound	Unbound
1dekB01	Unbound	Unbound	Unbound	Unbound	Unbound
1delA01	Unbound	Unbound	Unbound	Unbound	Unbound
1delB01	Unbound	Analogue:AMP	Unbound	Unbound	Unbound
1dekA02	Unbound	Unbound	Bound:DGP	Unbound	Unbound
1dekB02	Unbound	Unbound	Bound:DGP	Unbound	Unbound
1delA02	Unbound	Unbound	Bound:DGP	Unbound	Unbound
1delB02	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	LYS 10;LYS 14;ARG 177	ASP 15(Magnesium binding)
1dekB01	LYS 10;LYS 14;ARG 177	ASP 15(Magnesium binding)
1delA01	LYS 10;LYS 14;ARG 177	ASP 15(Magnesium binding)
1delB01	LYS 10;LYS 14;ARG 177	ASP 15(Magnesium binding)
1dekA02	ARG 68;ARG 132	TYR 42;GLN 85;GLU 108(non-cofactor magnesium binding)
1dekB02	ARG 68;ARG 132	TYR 42;GLN 85;GLU 108(non-cofactor magnesium binding)
1delA02	ARG 68;ARG 132	TYR 42;GLN 85;GLU 108(non-cofactor magnesium binding)
1delB02	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.

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