1N45

X-RAY CRYSTAL STRUCTURE OF HUMAN HEME OXYGENASE-1 (HO-1) IN COMPLEX WITH ITS SUBSTRATE HEME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.151 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Comparison of the heme-free and -bound crystal structures of human heme oxygenase-1.

Lad, L.Schuller, D.J.Shimizu, H.Friedman, J.Li, H.Ortiz de Montellano, P.R.Poulos, T.L.

(2003) J Biol Chem 278: 7834-7843

  • DOI: 10.1074/jbc.M211450200
  • Primary Citation of Related Structures:  
    1NI6, 1N3U, 1N45

  • PubMed Abstract: 
  • Heme oxygenase (HO) catalyzes the degradation of heme to biliverdin. The crystal structure of human HO-1 in complex with heme reveals a novel helical structure with conserved glycines in the distal helix, providing flexibility to accommodate substrate binding and product release (Schuller, D ...

    Heme oxygenase (HO) catalyzes the degradation of heme to biliverdin. The crystal structure of human HO-1 in complex with heme reveals a novel helical structure with conserved glycines in the distal helix, providing flexibility to accommodate substrate binding and product release (Schuller, D. J., Wilks, A., Ortiz de Montellano, P. R., and Poulos, T. L. (1999) Nat. Struct. Biol. 6, 860-867). To structurally understand the HO catalytic pathway in more detail, we have determined the crystal structure of human apo-HO-1 at 2.1 A and a higher resolution structure of human HO-1 in complex with heme at 1.5 A. Although the 1.5-A heme.HO-1 model confirms our initial analysis based on the 2.08-A model, the higher resolution structure has revealed important new details such as a solvent H-bonded network in the active site that may be important for catalysis. Because of the absence of the heme, the distal and proximal helices that bracket the heme plane in the holo structure move farther apart in the apo structure, thus increasing the size of the active-site pocket. Nevertheless, the relative positioning and conformation of critical catalytic residues remain unchanged in the apo structure compared with the holo structure, but an important solvent H-bonded network is missing in the apoenzyme. It thus appears that the binding of heme and a tightening of the structure around the heme stabilize the solvent H-bonded network required for proper catalysis.


    Related Citations: 
    • Crystal Structure of Human Heme Oxygenase-1
      Lad, L., Schuller, D.J., Friedman, J.P., Li, H., Ortiz de Montellano, P.R., Poulos, T.L.
      (1999) Nat Struct Biol 6: 903

    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Program in Macromolecular Structure, University of California, Irvine 92697, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
heme oxygenase 1A, B233Homo sapiensMutation(s): 0 
Gene Names: HMOX1HO1HO
EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
Find proteins for P09601 (Homo sapiens)
Explore P09601 
Go to UniProtKB:  P09601
NIH Common Fund Data Resources
PHAROS:  P09601
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
D [auth A], E [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.441α = 90
b = 54.534β = 99.05
c = 70.969γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MAGICSQUASHmodel building
AMoREphasing
SHELXL-97refinement
MAGICSQUASHphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references