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Structure of an orthorhombic crystal form of human cytosolic aconitase (IRP1)

Source organism: Homo sapiens
Biochemical function: 4 iron, 4 sulfur cluster binding
Biological process: intestinal absorption
Cellular component: extracellular exosome

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EC 4.2.1.3: Aconitate hydratase

Reaction catalysed:
(1a) citrate = cis-aconitate + H(2)O
Systematic name:
Citrate(isocitrate) hydro-lyase (cis-aconitate-forming)
Alternative Name(s):
  • 2-methylaconitate hydratase
  • AcnB
  • Aconitase
  • Cis-aconitase
  • Citrate hydro-lyase
  • Citrate(isocitrate) hydro-lyase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00694
Domain description: Aconitase C-terminal domain
Occurring in:
  1. Cytoplasmic aconitate hydratase
The deposited structure of PDB entry 2b3x contains 1 copy of Pfam domain PF00694 (Aconitase C-terminal domain) in Cytoplasmic aconitate hydratase. Showing 1 copy in chain A.

PF00330
Domain description: Aconitase family (aconitate hydratase)
Occurring in:
  1. Cytoplasmic aconitate hydratase
The deposited structure of PDB entry 2b3x contains 1 copy of Pfam domain PF00330 (Aconitase family (aconitate hydratase)) in Cytoplasmic aconitate hydratase. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR001030
Domain description: Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
Occurring in:
  1. Cytoplasmic aconitate hydratase
IPR018136
Domain description: Aconitase family, 4Fe-4S cluster binding site
Occurring in:
  1. Cytoplasmic aconitate hydratase
IPR006249
Domain description: Aconitase/Iron-responsive element-binding protein 2
Occurring in:
  1. Cytoplasmic aconitate hydratase
IPR015931
Domain description: Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3
Occurring in:
  1. Cytoplasmic aconitate hydratase
IPR000573
Domain description: Aconitase A/isopropylmalate dehydratase small subunit, swivel domain
Occurring in:
  1. Cytoplasmic aconitate hydratase
IPR044137
Domain description: Aconitase A, swivel domain
Occurring in:
  1. Cytoplasmic aconitate hydratase
IPR015928
Domain description: Aconitase/3-isopropylmalate dehydratase, swivel
Occurring in:
  1. Cytoplasmic aconitate hydratase
IPR036008
Domain description: Aconitase, iron-sulfur domain
Occurring in:
  1. Cytoplasmic aconitate hydratase

Structure domains

CATH CATH domains
3.30.499.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Aconitase; domain 3
Homology: Aconitase, domain 3
Occurring in:
  1. Cytoplasmic aconitate hydratase
The deposited structure of PDB entry 2b3x contains 2 copies of CATH domain 3.30.499.10 (Aconitase; domain 3) in Cytoplasmic aconitate hydratase. Showing 2 copies in chain A.
3.20.19.10
Class: Alpha Beta
Architecture: Alpha-Beta Barrel
Topology: Aconitase; domain 4
Homology: Aconitase, domain 4
Occurring in:
  1. Cytoplasmic aconitate hydratase
The deposited structure of PDB entry 2b3x contains 1 copy of CATH domain 3.20.19.10 (Aconitase; domain 4) in Cytoplasmic aconitate hydratase. Showing 1 copy in chain A.
6.10.190.10
Class: Special
Architecture: Helix non-globular
Topology: Apolipoprotein Cii; Chain: A;
Homology: Apolipoprotein Cii; Chain: A;
Occurring in:
  1. Cytoplasmic aconitate hydratase
The deposited structure of PDB entry 2b3x contains 1 copy of CATH domain 6.10.190.10 (Apolipoprotein Cii; Chain: A;) in Cytoplasmic aconitate hydratase. Showing 1 copy in chain A.
3.40.1060.10
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Aconitase; Domain 2
Homology: Aconitase, Domain 2
Occurring in:
  1. Cytoplasmic aconitate hydratase
The deposited structure of PDB entry 2b3x contains 1 copy of CATH domain 3.40.1060.10 (Aconitase; Domain 2) in Cytoplasmic aconitate hydratase. Showing 1 copy in chain A.
SCOP SCOP annotations
52017
Class: Alpha and beta proteins (a/b)
Fold: The "swivelling" beta/beta/alpha domain
Superfamily: LeuD/IlvD-like
Occurring in:
  1. Cytoplasmic aconitate hydratase
The deposited structure of PDB entry 2b3x contains 1 copy of SCOP domain 52017 (LeuD-like) in Cytoplasmic aconitate hydratase. Showing 1 copy in chain A.
53733
Class: Alpha and beta proteins (a/b)
Fold: Aconitase iron-sulfur domain
Superfamily: Aconitase iron-sulfur domain
Occurring in:
  1. Cytoplasmic aconitate hydratase
The deposited structure of PDB entry 2b3x contains 1 copy of SCOP domain 53733 (Aconitase iron-sulfur domain) in Cytoplasmic aconitate hydratase. Showing 1 copy in chain A.

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