1EYB | pdb_00001eyb

CRYSTAL STRUCTURE OF APO HUMAN HOMOGENTISATE DIOXYGENASE

• PDB DOI: https://doi.org/10.2210/pdb1EYB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-05-05 Released: 2000-11-05 
• Deposition Author(s): Timm, D.E., Titus, G.P., Penalva, M.A., Mueller, H.A., de Cordoba, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.222 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal structure of human homogentisate dioxygenase.

Titus, G.P., Mueller, H.A., Burgner, J., Rodriguez De Cordoba, S., Penalva, M.A., Timm, D.E.

(2000) Nat Struct Biol 7: 542-546

• PubMed: 10876237 
• DOI: https://doi.org/10.1038/76756
• Primary Citation Related Structures: 
  1EY2, 1EYB


• PubMed Abstract: 
  

  Homogentisate dioxygenase (HGO) cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. HGO deficiency causes alkaptonuria (AKU), the first human disease shown to be inherited as a recessive Mendelian trait. Crystal structures of apo-HGO and HGO containing an iron ion have been determined at 1.9 and 2.3 A resolution, respectively. The HGO protomer, which contains a 280-residue N-terminal domain and a 140-residue C-terminal domain, associates as a hexamer arranged as a dimer of trimers. The active site iron ion is coordinated near the interface between subunits in the HGO trimer by a Glu and two His side chains. HGO represents a new structural class of dioxygenases. The largest group of AKU associated missense mutations affect residues located in regions of contact between subunits.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 53.65 kDa 
• Atom Count: 3,786 
• Modeled Residue Count: 419 
• Deposited Residue Count: 471 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HOMOGENTISATE 1,2-DIOXYGENASE	A	471	Homo sapiens	Mutation(s): 10  EC: 1.13.11.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q93099 (Homo sapiens) Explore Q93099  Go to UniProtKB:  Q93099
PHAROS:  Q93099 GTEx:  ENSG00000113924

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.222 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.38	α = 90
b = 158.38	β = 90
c = 93.459	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
ADSC	data collection
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-05 
Deposition Author(s): Timm, D.E., Titus, G.P., Penalva, M.A., Mueller, H.A., de Cordoba, S.M.

Revision History  

• Version 1.0: 2000-11-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2015-06-24
  Changes: Data collection
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary