PDBsum entry 3vgv

Transferase

PDB id: 3vgv

Contents

Protein chains

(+ 8 more) 136 a.a.

129 a.a.

113 a.a.

Waters ×208

PDB id:

3vgv

Name:

Transferase

Title:

E134a mutant nucleoside diphosphate kinase derived from halomonas sp. 593

Structure:

Nucleoside diphosphate kinase. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p. Synonym: ndk, ndp kinase, nucleoside-2-p kinase. Engineered: yes. Mutation: yes

Source:

Halomonas. Organism_taxid: 195704. Strain: 593. Gene: ndk. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.218 R-free: 0.269

Authors:

N.Okazaki,Y.Yonezawa,S.Arai,F.Matsumoto,T.Tamada,H.Tokunaga, M.Ishibashi,M.Tokunaga,R.Kuroki

Key ref:

S.Arai et al. (2012). A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase. Protein Sci, 21, 498-510. PubMed id: 22275000

Date:

21-Aug-11 Release date: 11-Jul-12

Protein chains

Q83WH5  (Q83WH5_9GAMM) -  Nucleoside diphosphate kinase from Halomonas sp. #593

Seq: 141 a.a.

Struc: 136 a.a.*

Protein chain

Q83WH5  (Q83WH5_9GAMM) -  Nucleoside diphosphate kinase from Halomonas sp. #593

Seq: 141 a.a.

Struc: 129 a.a.*

Protein chain

Q83WH5  (Q83WH5_9GAMM) -  Nucleoside diphosphate kinase from Halomonas sp. #593

Seq: 141 a.a.

Struc: 113 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.2.7.4.6 - nucleoside-diphosphate kinase.
• Reaction:
  1. a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP
  2. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Protein Sci 21:498-510 (2012)

PubMed id: 22275000

A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase.

S.Arai, Y.Yonezawa, N.Okazaki, F.Matsumoto, T.Tamada, H.Tokunaga, M.Ishibashi, M.Blaber, M.Tokunaga, R.Kuroki.

ABSTRACT

No abstract given.