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Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate

Source organism: Neisseria gonorrhoeae NCCP11945
Biochemical function: metal ion binding
Biological process: nucleoside triphosphate biosynthetic process
Cellular component: cytoplasm

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EC 2.7.4.6: Nucleoside-diphosphate kinase

Reaction catalysed:
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Systematic name:
ATP:nucleoside-diphosphate phosphotransferase
Alternative Name(s):
  • NDK
  • Nucleoside 5'-diphosphate kinase
  • Nucleoside 5'-diphosphate phosphotransferase
  • Nucleoside diphosphate (UDP) kinase
  • Nucleoside diphosphokinase
  • Nucleotide phosphate kinase
  • UDP kinase
  • Uridine diphosphate kinase

GO terms

Sequence family

Pfam Protein family (Pfam)
PF00334
Domain description: Nucleoside diphosphate kinase
Occurring in:
  1. Nucleoside diphosphate kinase
The deposited structure of PDB entry 5v6d contains 16 copies of Pfam domain PF00334 (Nucleoside diphosphate kinase) in Nucleoside diphosphate kinase. Showing 1 copy in chain J.

InterPro InterPro annotations
IPR001564
Domain description: Nucleoside diphosphate kinase
Occurring in:
  1. Nucleoside diphosphate kinase
IPR034907
Domain description: Nucleoside diphosphate kinase-like domain
Occurring in:
  1. Nucleoside diphosphate kinase
IPR036850
Domain description: Nucleoside diphosphate kinase-like domain superfamily
Occurring in:
  1. Nucleoside diphosphate kinase
IPR023005
Domain description: Nucleoside diphosphate kinase, active site
Occurring in:
  1. Nucleoside diphosphate kinase

Structure domain

CATH CATH domain
3.30.70.141
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: Nucleoside diphosphate kinase-like domain
Occurring in:
  1. Nucleoside diphosphate kinase
The deposited structure of PDB entry 5v6d contains 16 copies of CATH domain 3.30.70.141 (Alpha-Beta Plaits) in Nucleoside diphosphate kinase. Showing 1 copy in chain F.

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