5BTQ

Crystal structure of human heme oxygenase 1 H25R with biliverdin bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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This is version 1.3 of the entry. See complete history. 


Literature

In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis

Sigala, P.A., Morante, K., Tsumoto, K., Caaveiro, J.M., Goldberg, D.E.

(2016) Biochemistry 55: 4836-4849

  • DOI: 10.1021/acs.biochem.6b00562
  • Primary Citation of Related Structures:  
    4WD4, 5BTQ

  • PubMed Abstract: 

    • Heme oxygenase (HO) is a ubiquitous enzyme with key roles in inflammation, cell signaling, heme disposal, and iron acquisition. HO catalyzes the oxidative conversion of heme to biliverdin (BV) using a conserved histidine to coordinate the iron atom of bound heme ...

    Heme oxygenase (HO) is a ubiquitous enzyme with key roles in inflammation, cell signaling, heme disposal, and iron acquisition. HO catalyzes the oxidative conversion of heme to biliverdin (BV) using a conserved histidine to coordinate the iron atom of bound heme. This His-heme interaction has been regarded as being essential for enzyme activity, because His-to-Ala mutants fail to convert heme to biliverdin in vitro. We probed a panel of proximal His mutants of cyanobacterial, human, and plant HO enzymes using a live-cell activity assay based on heterologous co-expression in Escherichia coli of each HO mutant and a fluorescent biliverdin biosensor. In contrast to in vitro studies with purified proteins, we observed that multiple HO mutants retained significant activity within the intracellular environment of bacteria. X-ray crystallographic structures of human HO1 H25R with bound heme and additional functional studies suggest that HO mutant activity inside these cells does not involve heme ligation by a proximal amino acid. Our study reveals unexpected plasticity in the active site binding interactions with heme that can support HO activity within cells, suggests important contributions by the surrounding active site environment to HO catalysis, and can guide efforts to understand the evolution and divergence of HO function.

    Organizational Affiliation: 

    Departments of Medicine and Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63110, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heme oxygenase 1A, B237Homo sapiensMutation(s): 1 
Gene Names: HMOX1, HO, HO1
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
BLA
Query on BLA
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.7α = 90
b = 54.74β = 99.37
c = 72.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Database references
  • Version 1.3: 2020-02-19
    Changes: Data collection, Database references, Derived calculations