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Crystal structure of NADP bound L-serine 3-dehydrogenase from Hyperthermophilic Archaeon Pyrobaculum calidifontis

Source organism: Pyrobaculum calidifontis JCM 11548
Biochemical function: NAD binding
Biological process: not assigned
Cellular component: not assigned

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EC 1.1.1.276: Serine 3-dehydrogenase (NADP(+))

Reaction catalysed:
(1a) L-serine + NADP(+) = 2-aminomalonate semialdehyde + NADPH
Systematic name:
L-serine:NADP(+) 3-oxidoreductase
Alternative Name(s):
  • Serine 3-dehydrogenase

GO terms

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Sequence families

Pfam Protein families (Pfam)
PF14833
Domain description: NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
Occurring in:
  1. 6-phosphogluconate dehydrogenase, NAD-binding protein
The deposited structure of PDB entry 3w6u contains 1 copy of Pfam domain PF14833 (NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase) in 6-phosphogluconate dehydrogenase, NAD-binding protein. Showing 1 copy in chain A.

PF03446
Domain description: NAD binding domain of 6-phosphogluconate dehydrogenase
Occurring in:
  1. 6-phosphogluconate dehydrogenase, NAD-binding protein
The deposited structure of PDB entry 3w6u contains 1 copy of Pfam domain PF03446 (NAD binding domain of 6-phosphogluconate dehydrogenase) in 6-phosphogluconate dehydrogenase, NAD-binding protein. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR029154
Domain description: 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain
Occurring in:
  1. 6-phosphogluconate dehydrogenase, NAD-binding protein
IPR013328
Domain description: 6-phosphogluconate dehydrogenase, domain 2
Occurring in:
  1. 6-phosphogluconate dehydrogenase, NAD-binding protein
IPR008927
Domain description: 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
Occurring in:
  1. 6-phosphogluconate dehydrogenase, NAD-binding protein
IPR002204
Domain description: 3-hydroxyisobutyrate dehydrogenase-related, conserved site
Occurring in:
  1. 6-phosphogluconate dehydrogenase, NAD-binding protein
IPR006115
Domain description: 6-phosphogluconate dehydrogenase, NADP-binding
Occurring in:
  1. 6-phosphogluconate dehydrogenase, NAD-binding protein
IPR036291
Domain description: NAD(P)-binding domain superfamily
Occurring in:
  1. 6-phosphogluconate dehydrogenase, NAD-binding protein
IPR015815
Domain description: 3-hydroxyisobutyrate dehydrogenase-related
Occurring in:
  1. 6-phosphogluconate dehydrogenase, NAD-binding protein

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, NAD-binding protein
The deposited structure of PDB entry 3w6u contains 1 copy of CATH domain 1.10.1040.10 (N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2) in 6-phosphogluconate dehydrogenase, NAD-binding protein. 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, NAD-binding protein
The deposited structure of PDB entry 3w6u contains 1 copy of CATH domain 3.40.50.720 (Rossmann fold) in 6-phosphogluconate dehydrogenase, NAD-binding protein. Showing 1 copy in chain A.

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