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Crystal Structure of Rat Peroxisomal Multifunctional enzyme Type-1 (RPMFE1) Complexed with Acetoacetyl-CoA and NAD

Source organism: Rattus norvegicus
Biochemical function: NAD+ binding
Biological process: fatty acid beta-oxidation
Cellular component: cytosol

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EC 5.3.3.8: Delta(3)-Delta(2)-enoyl-CoA isomerase

Reaction catalysed:
A (3E)-alk-3-enoyl-CoA = a (2E)-alk-2-enoyl-CoA
Systematic name:
(3Z/3E)-alk-3-enoyl-CoA (2E)-isomerase
Alternative Name(s):
  • 3,2-trans-enoyl-CoA isomerase
  • Acetylene-allene isomerase
  • Delta(3),Delta(2)-enoyl-CoA isomerase
  • Delta(3)-cis-Delta(2)-trans-enoyl-CoA isomerase
  • Dodecenoyl-CoA (3Z)-(2E)-isomerase
  • Dodecenoyl-CoA Delta(3)-cis-Delta(2)-trans-isomerase
  • Dodecenoyl-CoA Delta-isomerase
  • Dodecenoyl-CoA isomerase
  • ECI (gene name)

EC 4.2.1.17: Enoyl-CoA hydratase

Reaction catalysed:
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
Systematic name:
(3S)-3-hydroxyacyl-CoA hydro-lyase
Alternative Name(s):
  • 2-enoyl-CoA hydratase
  • 2-octenoyl coenzyme A hydrase
  • Acyl coenzyme A hydrase
  • Beta-hydroxyacid dehydrase
  • Beta-hydroxyacyl-CoA dehydrase
  • Crotonase
  • Crotonyl hydrase
  • D-3-hydroxyacyl-CoA dehydratase
  • ECH
  • Enol-CoA hydratase
  • Enoyl coenzyme A hydrase (D)
  • Enoyl coenzyme A hydrase (L)
  • Enoyl coenzyme A hydratase
  • Enoyl hydrase
  • Hydratase, enoyl coenzyme A
  • Short chain enoyl coenzyme A hydratase
  • Short-chain enoyl-CoA hydratase
  • Trans-2-enoyl-CoA hydratase
  • Unsaturated acyl-CoA hydratase

EC 1.1.1.35: 3-hydroxyacyl-CoA dehydrogenase

Reaction catalysed:
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
Systematic name:
(S)-3-hydroxyacyl-CoA:NAD(+) oxidoreductase
Alternative Name(s):
  • 1-specific DPN-linked beta-hydroxybutyric dehydrogenase
  • 3-L-hydroxyacyl-CoA dehydrogenase
  • 3-beta-hydroxyacyl coenzyme A dehydrogenase
  • 3-hydroxyacetyl-coenzyme A dehydrogenase
  • 3-hydroxyacyl coenzyme A dehydrogenase
  • 3-hydroxybutyryl-CoA dehydrogenase
  • 3-hydroxyisobutyryl-CoA dehydrogenase
  • 3-keto reductase
  • Beta-hydroxy acid dehydrogenase
  • Beta-hydroxyacyl CoA dehydrogenase
  • Beta-hydroxyacyl dehydrogenase
  • Beta-hydroxyacyl-coenzyme A synthetase
  • Beta-hydroxyacylcoenzyme A dehydrogenase
  • Beta-hydroxybutyrylcoenzyme A dehydrogenase
  • Beta-keto-reductase
  • Beta-ketoacyl-CoA reductase
  • L-3-hydroxyacyl CoA dehydrogenase
  • L-3-hydroxyacyl coenzyme A dehydrogenase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00725
Domain description: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
Occurring in:
  1. Peroxisomal bifunctional enzyme
The deposited structure of PDB entry 5mgb contains 4 copies of Pfam domain PF00725 (3-hydroxyacyl-CoA dehydrogenase, C-terminal domain) in Peroxisomal bifunctional enzyme. Showing 2 copies in chain A.

PF02737
Domain description: 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
Occurring in:
  1. Peroxisomal bifunctional enzyme
The deposited structure of PDB entry 5mgb contains 2 copies of Pfam domain PF02737 (3-hydroxyacyl-CoA dehydrogenase, NAD binding domain) in Peroxisomal bifunctional enzyme. Showing 1 copy in chain A.

PF00378
Domain description: Enoyl-CoA hydratase/isomerase
Occurring in:
  1. Peroxisomal bifunctional enzyme
The deposited structure of PDB entry 5mgb contains 2 copies of Pfam domain PF00378 (Enoyl-CoA hydratase/isomerase) in Peroxisomal bifunctional enzyme. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR008927
Domain description: 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
Occurring in:
  1. Peroxisomal bifunctional enzyme
IPR006108
Domain description: 3-hydroxyacyl-CoA dehydrogenase, C-terminal
Occurring in:
  1. Peroxisomal bifunctional enzyme
IPR006180
Domain description: 3-hydroxyacyl-CoA dehydrogenase, conserved site
Occurring in:
  1. Peroxisomal bifunctional enzyme
IPR006176
Domain description: 3-hydroxyacyl-CoA dehydrogenase, NAD binding
Occurring in:
  1. Peroxisomal bifunctional enzyme
IPR036291
Domain description: NAD(P)-binding domain superfamily
Occurring in:
  1. Peroxisomal bifunctional enzyme
IPR018376
Domain description: Enoyl-CoA hydratase/isomerase, conserved site
Occurring in:
  1. Peroxisomal bifunctional enzyme
IPR001753
Domain description: Enoyl-CoA hydratase/isomerase
Occurring in:
  1. Peroxisomal bifunctional enzyme
IPR029045
Domain description: ClpP/crotonase-like domain superfamily
Occurring in:
  1. Peroxisomal bifunctional enzyme

Structure domains

CATH CATH domains
1.10.1040.50
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. Peroxisomal bifunctional enzyme
The deposited structure of PDB entry 5mgb contains 2 copies of CATH domain 1.10.1040.50 (N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2) in Peroxisomal bifunctional enzyme. 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. Peroxisomal bifunctional enzyme
The deposited structure of PDB entry 5mgb contains 2 copies of CATH domain 3.40.50.720 (Rossmann fold) in Peroxisomal bifunctional enzyme. Showing 1 copy in chain A.
3.90.226.10
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: 2-enoyl-CoA Hydratase; Chain A, domain 1
Homology: 2-enoyl-CoA Hydratase; Chain A, domain 1
Occurring in:
  1. Peroxisomal bifunctional enzyme
The deposited structure of PDB entry 5mgb contains 2 copies of CATH domain 3.90.226.10 (2-enoyl-CoA Hydratase; Chain A, domain 1) in Peroxisomal bifunctional enzyme. Showing 1 copy in chain A.

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