1WE1 | pdb_00001we1

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

• PDB DOI: https://doi.org/10.2210/pdb1WE1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-05-21 Released: 2004-12-21 
• Deposition Author(s): Sugishima, M., Migita, C.T., Zhang, X., Yoshida, T., Fukuyama, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.269 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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

• PubMed: 15560792 
• DOI: https://doi.org/10.1111/j.1432-1033.2004.04411.x
• Primary Citation Related Structures: 
  1WE1


• 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, 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.

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Organizational Affiliation: 
• Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 111.65 kDa 
• Atom Count: 7,468 
• Modeled Residue Count: 887 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme oxygenase 1	A, B, C, D	240	Synechocystis sp. PCC 6803	Mutation(s): 0  EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt
Find proteins for P72849 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P72849  Go to UniProtKB:  P72849

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	H [auth A], M [auth B], Q [auth C], U [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PO4	E [auth A], K [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
IPA	I [auth A], J [auth A], N [auth B], O [auth B], R [auth C], S [auth C], V [auth D], W [auth D]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL	F [auth A], G [auth A], L [auth B], P [auth C], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.269 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.79	α = 90
b = 113.73	β = 112.26
c = 109.7	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Sugishima, M., Migita, C.T., Zhang, X., Yoshida, T., Fukuyama, K.

Revision History  

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description