1TWR

Crystal structures of ferrous and ferrous-NO forms of verdoheme in a complex with human heme oxygenase-1: catalytic implications for heme cleavage

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.241 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structures of ferrous and ferrous-NO forms of verdoheme in a complex with human heme oxygenase-1: catalytic implications for heme cleavage.

Lad, L., Ortiz de Montellano, P.R., Poulos, T.L.

(2004) J Inorg Biochem 98: 1686-1695

  • DOI: 10.1016/j.jinorgbio.2004.07.004
  • Primary Citation of Related Structures:  
    1TWN, 1TWR

  • PubMed Abstract: 

    • Heme oxygenase oxidatively degrades heme to biliverdin resulting in the release of iron and CO through a process in which the heme participates both as a cofactor and substrate. One of the least understood steps in the heme degradation pathway is the conversion of verdoheme to biliverdin ...

    Heme oxygenase oxidatively degrades heme to biliverdin resulting in the release of iron and CO through a process in which the heme participates both as a cofactor and substrate. One of the least understood steps in the heme degradation pathway is the conversion of verdoheme to biliverdin. In order to obtain a better understanding of this step we report the crystal structures of ferrous-verdoheme and, as a mimic for the oxy-verdoheme complex, ferrous-NO verdoheme in a complex with human HO-1 at 2.20 and 2.10 A, respectively. In both structures the verdoheme occupies the same binding location as heme in heme-HO-1, but rather than being ruffled verdoheme in both sets of structures is flat. Both structures are similar to their heme counterparts except for the distal helix and heme pocket solvent structure. In the ferrous-verdoheme structure the distal helix moves closer to the verdoheme, thus tightening the active site. NO binds to verdoheme in a similar bent conformation to that found in heme-HO-1. The bend angle in the verodoheme-NO structure places the terminal NO oxygen 1 A closer to the alpha-meso oxygen of verdoheme compared to the alpha-meso carbon on the heme-NO structure. A network of water molecules, which provide the required protons to activate the iron-oxy complex of heme-HO-1, is absent in both ferrous-verdoheme and the verdoheme-NO structure.

    Organizational Affiliation: 

    Department of Molecular Biology and Biochemistry, University of California, 2206 Natural Sciences 1, Irvine, CA 92697-3900, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heme oxygenase 1A, B233Homo sapiensMutation(s): 0 
Gene Names: HMOX1, HO1, HO
EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09601 (Homo sapiens)
Explore P09601 
Go to UniProtKB:  P09601
PHAROS:  P09601
GTEx:  ENSG00000100292 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09601
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VER
Query on VER
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		IRON-OCTAETHYLPORPHYRIN
C30 H27 Fe N4 O3
TXPACERVXXBEPS-YLPJGRDPDP		 Ligand Interaction
NO
Query on NO
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYAM		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.038α = 90
b = 54.258β = 98.12
c = 70.249γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance