Function and Biology

Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A

Source organism: Homo sapiens
Biochemical function: NADP binding
Biological process: D-gluconate catabolic process
Cellular component: extracellular exosome

EC 1.1.1.44: Phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)

Reaction catalysed:
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH
Systematic name:
6-phospho-D-gluconate:NADP(+) 2-oxidoreductase (decarboxylating)
Alternative Name(s):
  • 6-phospho-D-gluconate dehydrogenase
  • 6-phosphogluconate dehydrogenase (decarboxylating)
  • 6-phosphogluconic carboxylase
  • 6-phosphogluconic dehydrogenase
  • 6PGD
  • Phosphogluconic acid dehydrogenase

Sequence families

Pfam Protein families (Pfam)
PF00393
Domain description: 6-phosphogluconate dehydrogenase, C-terminal domain
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
The deposited structure of PDB entry 2jkv contains 6 copies of Pfam domain PF00393 (6-phosphogluconate dehydrogenase, C-terminal domain) in 6-phosphogluconate dehydrogenase, decarboxylating. Showing 1 copy in chain A.

PF03446
Domain description: NAD binding domain of 6-phosphogluconate dehydrogenase
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
The deposited structure of PDB entry 2jkv contains 6 copies of Pfam domain PF03446 (NAD binding domain of 6-phosphogluconate dehydrogenase) in 6-phosphogluconate dehydrogenase, decarboxylating. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR006183
Domain description: 6-phosphogluconate dehydrogenase
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
IPR006114
Domain description: 6-phosphogluconate dehydrogenase, C-terminal
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
IPR006113
Domain description: 6-phosphogluconate dehydrogenase, decarboxylating
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
IPR006184
Domain description: 6-phosphogluconate-binding site
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
IPR013328
Domain description: 6-phosphogluconate dehydrogenase, domain 2
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
IPR008927
Domain description: 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
IPR006115
Domain description: 6-phosphogluconate dehydrogenase, NADP-binding
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
IPR036291
Domain description: NAD(P)-binding domain superfamily
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
IPR029039
Domain description: Flavoprotein-like superfamily
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating

Structure domains

CATH CATH domains
1.10.1040.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homology: N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
The deposited structure of PDB entry 2jkv contains 6 copies of CATH domain 1.10.1040.10 (N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2) in 6-phosphogluconate dehydrogenase, decarboxylating. Showing 1 copy in chain A.
3.40.50.720
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: NAD(P)-binding Rossmann-like Domain
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
The deposited structure of PDB entry 2jkv contains 6 copies of CATH domain 3.40.50.720 (Rossmann fold) in 6-phosphogluconate dehydrogenase, decarboxylating. Showing 1 copy in chain A.
1.20.5.320
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homology: 6-Phosphogluconate Dehydrogenase, domain 3
Occurring in:
  1. 6-phosphogluconate dehydrogenase, decarboxylating
The deposited structure of PDB entry 2jkv contains 5 copies of CATH domain 1.20.5.320 (Single alpha-helices involved in coiled-coils or other helix-helix interfaces) in 6-phosphogluconate dehydrogenase, decarboxylating. Showing 1 copy in chain A.