2Q32 | pdb_00002q32

Crystal structure of human heme oxygenase-2 C127A (HO-2)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.253 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Literature

Comparison of Apo- and Heme-bound Crystal Structures of a Truncated Human Heme Oxygenase-2.

Bianchetti, C.M., Yi, L., Ragsdale, S.W., Phillips Jr., G.N.

(2007) J Biological Chem 282: 37624-37631

  • DOI: https://doi.org/10.1074/jbc.M707396200
  • Primary Citation Related Structures: 
    2Q32, 2QPP, 2RGZ

  • PubMed Abstract: 

    Heme oxygenase (HO) catalyzes the first step in the heme degradation pathway. The crystal structures of apo- and heme-bound truncated human HO-2 reveal a primarily alpha-helical architecture similar to that of human HO-1 and other known HOs. Proper orientation of heme in HO-2 is required for the regioselective oxidation of the alpha-mesocarbon. This is accomplished by interactions within the heme binding pocket, which is made up of two helices. The iron coordinating residue, His(45), resides on the proximal helix. The distal helix contains highly conserved glycine residues that allow the helix to flex and interact with the bound heme. Tyr(154), Lys(199), and Arg(203) orient the heme through direct interactions with the heme propionates. The rearrangements of side chains in heme-bound HO-2 compared with apoHO-2 further elucidate HO-2 heme interactions.

    • Organizational Affiliation: 
    • Graduate Program in Biophysics, Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA.

Macromolecule Content 

  • Total Structure Weight: 62.28 kDa 
  • Atom Count: 3,843 
  • Modeled Residue Count: 431 
  • Deposited Residue Count: 528 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heme oxygenase 2
A, B
264Homo sapiensMutation(s): 1 
Gene Names: Hs.284279, HMOX2, HO2
EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30519 (Homo sapiens)
Explore P30519 
Go to UniProtKB:  P30519
PHAROS:  P30519
GTEx:  ENSG00000103415 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30519
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.769α = 90
b = 86.017β = 90
c = 97.753γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-01-15
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description