spacer
spacer

PDBsum entry 1wow

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1wow
Jmol PyMol
Contents
Protein chains
245 a.a. *
Ligands
HEM ×2
Waters ×469
* Residue conservation analysis
PDB id:
1wow
Name: Oxidoreductase
Title: Crystal structure of heme oxygenase-2 from synechocystis sp. Complexed with heme in ferrous form
Structure: Heme oxygenase 2. Chain: a, b. Engineered: yes
Source: Synechocystis sp.. Organism_taxid: 1148. Strain: pcc 6803. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.219     R-free:   0.282
Authors: M.Sugishima,Y.Hagiwara,X.Zhang,T.Yoshida,C.T.Migita,K.Fukuya
Key ref:
M.Sugishima et al. (2005). Crystal structure of dimeric heme oxygenase-2 from Synechocystis sp. PCC 6803 in complex with heme. Biochemistry, 44, 4257-4266. PubMed id: 15766254 DOI: 10.1021/bi0480483
Date:
26-Aug-04     Release date:   22-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P74133  (HO2_SYNY3) -  Heme oxygenase 2
Seq:
Struc:
250 a.a.
245 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.14.18  - Heme oxygenase (biliverdin-producing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protoheme + 3 [reduced NADPH--hemoprotein reductase] + 3 O2 = biliverdin + Fe2+ + CO + 3 [oxidized NADPH--hemoprotein reductase] + 3 H2O
Protoheme
Bound ligand (Het Group name = HEM)
matches with 95.45% similarity
+ 3 × [reduced NADPH--hemoprotein reductase]
+ 3 × O(2)
= biliverdin
+ Fe(2+)
+ CO
+ 3 × [oxidized NADPH--hemoprotein reductase]
+ 3 × H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     oxidation-reduction process   6 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi0480483 Biochemistry 44:4257-4266 (2005)
PubMed id: 15766254  
 
 
Crystal structure of dimeric heme oxygenase-2 from Synechocystis sp. PCC 6803 in complex with heme.
M.Sugishima, Y.Hagiwara, X.Zhang, T.Yoshida, C.T.Migita, K.Fukuyama.
 
  ABSTRACT  
 
Phycobiliproteins, light-harvesting proteins in cyanobacteria, red algae, and cryptophytes, contain phycobilin pigments. Phycobilins are synthesized from biliverdin, which is produced by the oxidative cleavage of the heme porphyrin ring catalyzed by heme oxygenase (HO). Two paralogs of ho (ho1 and ho2) have been identified in the genome of the cyanobacterium, Synechocystis sp. PCC 6803. The recombinant proteins of both paralogs (Syn HO-1 and Syn HO-2) possess in vitro heme degradation activity. We have determined the crystal structures of Syn HO-2 in complex with heme (heme-Syn HO-2) and its reduced and NO bound forms. The heme-Syn HO-2 crystal was a nonmerohedral twin, and detwinned diffraction data were used to refine the structure. Although heme-Syn HO-2 shares common folding with other HOs, the C-terminal segment is ordered and turns back to the heme-binding side. Gel-filtration chromatography analysis and molecular packing in the crystal indicate that heme-Syn HO-2 forms a homodimer, in which the C-terminal ordered segments interact with each other. Because Syn HO-2 is a monomer in the apo state, the dimeric interaction may aid in the selection of the reducing partner but likely does not interfere with heme binding. The heme iron is coordinated by a water molecule in the ferric form, but the distal water is absent in the ferrous form. In all of the Syn HO-2 structures, several water molecules form a hydrogen-bond network at the distal hemepocket, which is involved in HO activity. Upon NO binding, the side-chain conformation of Tyr 156 changes. Tyr 156 is located at the hydrophobic cluster, which interrupts the possible H(+) pathway from the molecular surface to the hemepocket. Thus, Tyr 156 may function as a H(+) shuttle by changing conformation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21250783 M.E.Auldridge, and K.T.Forest (2011).
Bacterial phytochromes: More than meets the light.
  Crit Rev Biochem Mol Biol, 46, 67-88.  
19860740 B.Gisk, Y.Yasui, T.Kohchi, and N.Frankenberg-Dinkel (2010).
Characterization of the haem oxygenase protein family in Arabidopsis thaliana reveals a diversity of functions.
  Biochem J, 425, 425-434.  
20378668 G.S.Shekhawat, and K.Verma (2010).
Haem oxygenase (HO): an overlooked enzyme of plant metabolism and defence.
  J Exp Bot, 61, 2255-2270.  
20414806 R.S.Gupta (2010).
Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups.
  Photosynth Res, 104, 357-372.  
20194361 T.Goto, R.Aoki, K.Minamizaki, and Y.Fujita (2010).
Functional differentiation of two analogous coproporphyrinogen III oxidases for heme and chlorophyll biosynthesis pathways in the cyanobacterium Synechocystis sp. PCC 6803.
  Plant Cell Physiol, 51, 650-663.  
19887371 Y.Hagiwara, M.Sugishima, H.Khawn, H.Kinoshita, K.Inomata, L.Shang, J.C.Lagarias, Y.Takahashi, and K.Fukuyama (2010).
Structural insights into vinyl reduction regiospecificity of phycocyanobilin:ferredoxin oxidoreductase (PcyA).
  J Biol Chem, 285, 1000-1007.
PDB codes: 3i8u 3i94 3i95
19542007 J.Hedger, P.C.Holmquist, K.A.Leigh, K.Saraff, C.Pomykal, and M.L.Summers (2009).
Illumination stimulates cAMP receptor protein-dependent transcriptional activation from regulatory regions containing class I and class II promoter elements in Synechocystis sp. PCC 6803.
  Microbiology, 155, 2994-3004.  
18846276 T.Dammeyer, and N.Frankenberg-Dinkel (2008).
Function and distribution of bilin biosynthesis enzymes in photosynthetic organisms.
  Photochem Photobiol Sci, 7, 1121-1130.  
17965015 C.M.Bianchetti, L.Yi, S.W.Ragsdale, and G.N.Phillips (2007).
Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2.
  J Biol Chem, 282, 37624-37631.
PDB codes: 2q32 2qpp 2rgz
17534530 M.Unno, T.Matsui, and M.Ikeda-Saito (2007).
Structure and catalytic mechanism of heme oxygenase.
  Nat Prod Rep, 24, 553-570.  
16817889 P.J.Linley, M.Landsberger, T.Kohchi, J.B.Cooper, and M.J.Terry (2006).
The molecular basis of heme oxygenase deficiency in the pcd1 mutant of pea.
  FEBS J, 273, 2594-2606.  
16914546 S.Jantaro, Q.Ali, S.Lone, and Q.He (2006).
Suppression of the lethality of high light to a quadruple HLI mutant by the inactivation of the regulatory protein PfsR in Synechocystis PCC 6803.
  J Biol Chem, 281, 30865-30874.  
17076701 T.Gohya, X.Zhang, T.Yoshida, and C.T.Migita (2006).
Spectroscopic characterization of a higher plant heme oxygenase isoform-1 from Glycine max (soybean)--coordination structure of the heme complex and catabolism of heme.
  FEBS J, 273, 5384-5399.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

spacer

spacer