Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.19 kDa 
• Atom Count: 3431 
• Modelled Residue Count: 401 
• Deposited Residue Count: 466 
• Unique protein chains: 1

1T5P

Human Heme Oxygenase Oxidation of alpha- and gamma-meso-phenylhemes

• DOI: 10.2210/pdb1T5P/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-05-05 Released: 2004-08-24 
• Deposition Author(s): Wang, J., Niemevz, F., Lad, L., Buldain, G., Poulos, T.L., Ortiz de Montellano, P.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.310 
• R-Value Work: 0.270 

Literature

Human heme oxygenase oxidation of 5- and 15-phenylhemes.

Wang, J., Niemevz, F., Lad, L., Huang, L., Alvarez, D.E., Buldain, G., Poulos, T.L., Ortiz de Montellano, P.R.

(2004) J Biol Chem 279: 42593-42604

• PubMed: 15297453 
• DOI: 10.1074/jbc.M406346200
• Primary Citation of Related Structures:  
  1S13, 1T5P


• PubMed Abstract: 
  

Human heme oxygenase-1 (hHO-1) catalyzes the O2-dependent oxidation of heme to biliverdin, CO, and free iron. Previous work indicated that electrophilic addition of the terminal oxygen of the ferric hydroperoxo complex to the alpha-meso-carbon gives 5-hydroxyheme. Earlier efforts to block this reaction with a 5-methyl substituent failed, as the reaction still gave biliverdin IXalpha. Surprisingly, a 15-methyl substituent caused exclusive cleavage at the gamma-meso-rather than at the normal, unsubstituted alpha-meso-carbon. No CO was formed in these reactions, but the fragment cleaved from the porphyrin eluded identification. We report here that hHO-1 cleaves 5-phenylheme to biliverdin IXalpha and oxidizes 15-phenylheme at the alpha-meso position to give 10-phenylbiliverdin IXalpha. The fragment extruded in the oxidation of 5-phenylheme is benzoic acid, one oxygen of which comes from O2 and the other from water. The 2.29- and 2.11-A crystal structures of the hHO-1 complexes with 1- and 15-phenylheme, respectively, show clear electron density for both the 5- and 15-phenyl rings in both molecules of the asymmetric unit. The overall structure of 15-phenylheme-hHO-1 is similar to that of heme-hHO-1 except for small changes in distal residues 141-150 and in the proximal Lys18 and Lys22. In the 5-phenylheme-hHO-1 structure, the phenyl-substituted heme occupies the same position as heme in the heme-HO-1 complex but the 5-phenyl substituent disrupts the rigid hydrophobic wall of residues Met34, Phe214, and residues 26-42 near the alpha-meso carbon. The results provide independent support for an electrophilic oxidation mechanism and support a role for stereochemical control of the reaction regiospecificity.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-2280, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme oxygenase 1	A, B	233	Homo sapiens	Mutation(s): 0  Gene Names: HMOX1, HO1, HO 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 GTEx:  ENSG00000100292

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1FH	C [auth A], D [auth B]	12-PHENYLHEME C40 H38 Fe N4 O4 QYZKGXFDXHPSJI-SZSVFXIKDE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.310 
• R-Value Work: 0.270 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.914	α = 90
b = 64.425	β = 90.02
c = 60.467	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-05 
• Released Date: 2004-08-24 
Deposition Author(s): Wang, J., Niemevz, F., Lad, L., Buldain, G., Poulos, T.L., Ortiz de Montellano, P.R.

Revision History  

• Version 1.0: 2004-08-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance