1WE1

Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC6803 in complex with heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme

Sugishima, M.Migita, C.T.Zhang, X.Yoshida, T.Fukuyama, K.

(2004) Eur.J.Biochem. 271: 4517-4525

  • DOI: 10.1111/j.1432-1033.2004.04411.x

  • PubMed Abstract: 
  • Heme oxygenase (HO) catalyzes the oxidative degradation of heme utilizing molecular oxygen and reducing equivalents. In photosynthetic organisms, HO functions in the biosynthesis of such open-chain tetrapyrroles as phyto-chromobilin and phycobilins, ...

    Heme oxygenase (HO) catalyzes the oxidative degradation of heme utilizing molecular oxygen and reducing equivalents. In photosynthetic organisms, HO functions in the biosynthesis of such open-chain tetrapyrroles as phyto-chromobilin and phycobilins, which are involved in the signal transduction for light responses and light harvesting for photosynthesis, respectively. We have determined the first crystal structure of a HO-1 from a photosynthetic organism, Synechocystis sp. PCC 6803 (Syn HO-1), in complex with heme at 2.5 A resolution. Heme-Syn HO-1 shares a common folding with other heme-HOs. Although the heme pocket of heme-Syn HO-1 is, for the most part, similar to that of mammalian HO-1, they differ in such features as the flexibility of the distal helix and hydrophobicity. In addition, 2-propanol derived from the crystallization solution occupied the hydrophobic cavity, which is proposed to be a CO trapping site in rat HO-1 that suppresses product inhibition. Although Syn HO-1 and mammalian HO-1 are similar in overall structure and amino acid sequence (57% similarity vs. human HO-1), their molecular surfaces differ in charge distribution. The surfaces of the heme binding sides are both positively charged, but this patch of Syn HO-1 is narrow compared to that of mammalian HO-1. This feature is suited to the selective binding of ferredoxin, the physiological redox partner of Syn HO-1; the molecular size of ferredoxin is approximately 10 kDa whereas the size of NADPH-cytochrome P450 reductase, a reducing partner of mammalian HO-1, is approximately 77 kDa. A docking model of heme-Syn HO-1 and ferredoxin suggests indirect electron transfer from an iron-sulfur cluster in ferredoxin to the heme iron of heme-Syn HO-1.


    Related Citations: 
    • Expression and characterization of cyanobacterium heme oxygenase, a key enzyme in the phycobilin synthesis. Properties of the heme complex of recombinant active enzyme
      Migita, C.T.,Zhang, X.,Yoshida, T.
      (2003) Eur.J.Biochem. 270: 687


    Organizational Affiliation

    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heme oxygenase 1
A, B, C, D
240Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: pbsA1
EC: 1.14.14.18
Find proteins for P72849 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P72849
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
A, B, C, D
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.790α = 90.00
b = 113.730β = 112.26
c = 109.700γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
SCALAdata scaling
CCP4data scaling
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance