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The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex.

Source organism: Homo sapiens
Biochemical function: flavin adenine dinucleotide binding
Biological process: acetyl-CoA biosynthetic process from pyruvate
Cellular component: pyruvate dehydrogenase complex

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EC 1.8.1.4: Dihydrolipoyl dehydrogenase

Reaction catalysed:
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
Systematic name:
Protein-N(6)-(dihydrolipoyl)lysine:NAD(+) oxidoreductase
Alternative Name(s):
  • Dehydrolipoate dehydrogenase
  • Diaphorase
  • Dihydrolipoamide dehydrogenase
  • Dihydrolipoamide:NAD(+) oxidoreductase
  • Dihydrolipoic dehydrogenase
  • Dihydrothioctic dehydrogenase
  • E3 component of alpha-ketoacid dehydrogenase complexes
  • Glycine-cleavage system L-protein
  • L-protein
  • LDP-Glc
  • LDP-Val
  • Lipoamide dehydrogenase (NADH)
  • Lipoamide oxidoreductase (NADH)
  • Lipoamide reductase
  • Lipoamide reductase (NADH)
  • Lipoate dehydrogenase
  • Lipoic acid dehydrogenase
  • Lipoyl dehydrogenase
  • Protein-6-N-(dihydrolipoyl)lysine:NAD(+) oxidoreductase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF02852
Domain description: Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
The deposited structure of PDB entry 1zy8 contains 10 copies of Pfam domain PF02852 (Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain) in Dihydrolipoyl dehydrogenase, mitochondrial. Showing 1 copy in chain A.

PF07992
Domain description: Pyridine nucleotide-disulphide oxidoreductase
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
The deposited structure of PDB entry 1zy8 contains 10 copies of Pfam domain PF07992 (Pyridine nucleotide-disulphide oxidoreductase) in Dihydrolipoyl dehydrogenase, mitochondrial. Showing 1 copy in chain A.

PF02817
Domain description: e3 binding domain
Occurring in:
  1. Pyruvate dehydrogenase protein X component, mitochondrial
The deposited structure of PDB entry 1zy8 contains 5 copies of Pfam domain PF02817 (e3 binding domain) in Pyruvate dehydrogenase protein X component, mitochondrial. Showing 1 copy in chain K.

PF00364
Domain description: Biotin-requiring enzyme
Occurring in:
  1. Pyruvate dehydrogenase protein X component, mitochondrial
The deposited structure of PDB entry 1zy8 contains 5 copies of Pfam domain PF00364 (Biotin-requiring enzyme) in Pyruvate dehydrogenase protein X component, mitochondrial. Showing 1 copy in chain K (this domain is out of the observed residue ranges!).

InterPro InterPro annotations
IPR036188
Domain description: FAD/NAD(P)-binding domain superfamily
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
IPR016156
Domain description: FAD/NAD-linked reductase, dimerisation domain superfamily
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
IPR004167
Domain description: Peripheral subunit-binding domain
Occurring in:
  1. Pyruvate dehydrogenase protein X component, mitochondrial
IPR036625
Domain description: E3-binding domain superfamily
Occurring in:
  1. Pyruvate dehydrogenase protein X component, mitochondrial
IPR000089
Domain description: Biotin/lipoyl attachment
Occurring in:
  1. Pyruvate dehydrogenase protein X component, mitochondrial
IPR004099
Domain description: Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
IPR012999
Domain description: Pyridine nucleotide-disulphide oxidoreductase, class I, active site
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
IPR023753
Domain description: FAD/NAD(P)-binding domain
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
IPR006258
Domain description: Dihydrolipoamide dehydrogenase
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
IPR001100
Domain description: Pyridine nucleotide-disulphide oxidoreductase, class I
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
IPR003016
Domain description: 2-oxo acid dehydrogenase, lipoyl-binding site
Occurring in:
  1. Pyruvate dehydrogenase protein X component, mitochondrial
IPR045257
Domain description: Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component
Occurring in:
  1. Pyruvate dehydrogenase protein X component, mitochondrial
IPR011053
Domain description: Single hybrid motif
Occurring in:
  1. Pyruvate dehydrogenase protein X component, mitochondrial

Structure domains

CATH CATH domains
3.50.50.60
Class: Alpha Beta
Architecture: 3-Layer(bba) Sandwich
Topology: FAD/NAD(P)-binding domain
Homology: FAD/NAD(P)-binding domain
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
The deposited structure of PDB entry 1zy8 contains 20 copies of CATH domain 3.50.50.60 (FAD/NAD(P)-binding domain) in Dihydrolipoyl dehydrogenase, mitochondrial. Showing 2 copies in chain A.
3.30.390.30
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Enolase-like; domain 1
Homology: Enolase-like; domain 1
Occurring in:
  1. Dihydrolipoyl dehydrogenase, mitochondrial
The deposited structure of PDB entry 1zy8 contains 10 copies of CATH domain 3.30.390.30 (Enolase-like; domain 1) in Dihydrolipoyl dehydrogenase, mitochondrial. Showing 1 copy in chain A.
4.10.320.10
Class: Few Secondary Structures
Architecture: Irregular
Topology: Dihydrolipoamide Transferase
Homology: E3-binding domain
Occurring in:
  1. Pyruvate dehydrogenase protein X component, mitochondrial
The deposited structure of PDB entry 1zy8 contains 5 copies of CATH domain 4.10.320.10 (Dihydrolipoamide Transferase) in Pyruvate dehydrogenase protein X component, mitochondrial. Showing 1 copy in chain K.

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