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PDBsum entry 1qwm

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1qwm
Jmol
Contents
Protein chains
490 a.a. *
Ligands
AZI
HEM-FMT
FMT ×35
HEM
Waters ×933
* Residue conservation analysis
PDB id:
1qwm
Name: Oxidoreductase
Title: Structure of helicobacter pylori catalase with formic acid b
Structure: Kata catalase. Chain: a, b. Engineered: yes
Source: Helicobacter pylori. Organism_taxid: 210. Gene: kata (hp0875). Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.60Å     R-factor:   0.196     R-free:   0.227
Authors: P.C.Loewen,X.Carpena,R.Perez-Luque,C.Rovira,R.Haas,S.Odenbre P.Nicholls,I.Fita
Key ref:
P.C.Loewen et al. (2004). Structure of Helicobacter pylori catalase, with and without formic acid bound, at 1.6 A resolution. Biochemistry, 43, 3089-3103. PubMed id: 15023060 DOI: 10.1021/bi035663i
Date:
02-Sep-03     Release date:   30-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P77872  (CATA_HELPY) -  Catalase
Seq:
Struc:
505 a.a.
490 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.6  - Catalase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 H2O2 = O2 + 2 H2O
2 × H(2)O(2)
= O(2)
+ 2 × H(2)O
      Cofactor: Heme; Mn(2+)
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     protein binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi035663i Biochemistry 43:3089-3103 (2004)
PubMed id: 15023060  
 
 
Structure of Helicobacter pylori catalase, with and without formic acid bound, at 1.6 A resolution.
P.C.Loewen, X.Carpena, C.Rovira, A.Ivancich, R.Perez-Luque, R.Haas, S.Odenbreit, P.Nicholls, I.Fita.
 
  ABSTRACT  
 
Helicobacter pylori produces one monofunctional catalase, encoded by katA (hp0875). The crystal structure of H. pylori catalase (HPC) has been determined and refined at 1.6 A with crystallographic agreement factors R and R(free) of 17.4 and 21.9%, respectively. The crystal exhibits P2(1)2(1)2 space group symmetry and contains two protein subunits in the asymmetric unit. The core structure of the HPC subunit, including the disposition of a heme b prosthetic group, is closely related to those of other catalases, although it appears to be the only clade III catalase that has been characterized that does not bind NADPH. The heme iron in one subunit of the native enzyme appears to be covalently modified, possibly with a perhydroxy or dioxygen group in a compound III-like structure. Formic acid is known to bind in the active site of catalases, promoting the breakdown of reaction intermediates compound I and compound II. The structure of an HPC crystal soaked with sodium formate at pH 5.6 has also been determined to 1.6 A (with R and R(free) values of 18.1 and 20.7%, respectively), revealing at least 36 separate formate or formic acid residues in the HPC dimer. In turn, the number of water molecules refined into the models decreased from 1016 in the native enzyme to 938 in the formate-treated enzyme. Extra density, interpreted as azide, is found in a location of both structures that involves interaction with all four subunits in the tetramer. Electron paramagnetic resonance spectra confirm that azide does not bind as a ligand of the iron and that formate does bind in the heme pocket. The stability of the formate or formic acid molecule found inside the heme distal pocket has been investigated by calculations based on density functional theory.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19290552 B.Wiseman, J.Colin, A.T.Smith, A.Ivancich, and P.C.Loewen (2009).
Mechanistic insight into the initiation step of the reaction of Burkholderia pseudomallei catalase-peroxidase with peroxyacetic acid.
  J Biol Inorg Chem, 14, 801-811.  
19369943 J.Cao, J.Schulte, A.Knight, N.R.Leslie, A.Zagozdzon, R.Bronson, Y.Manevich, C.Beeson, and C.A.Neumann (2009).
Prdx1 inhibits tumorigenesis via regulating PTEN/AKT activity.
  EMBO J, 28, 1505-1517.  
19827095 S.Pakhomova, B.Gao, W.E.Boeglin, A.R.Brash, and M.E.Newcomer (2009).
The structure and peroxidase activity of a 33-kDa catalase-related protein from Mycobacterium avium ssp. paratuberculosis.
  Protein Sci, 18, 2559-2568.
PDB codes: 3e4w 3e4y
17242507 E.K.Riise, M.S.Lorentzen, R.Helland, A.O.Smalås, H.K.Leiros, and N.P.Willassen (2007).
The first structure of a cold-active catalase from Vibrio salmonicida at 1.96 A reveals structural aspects of cold adaptation.
  Acta Crystallogr D Biol Crystallogr, 63, 135-148.
PDB code: 2isa
17318598 M.A.Carrondo, I.Bento, P.M.Matias, and P.F.Lindley (2007).
Crystallographic evidence for dioxygen interactions with iron proteins.
  J Biol Inorg Chem, 12, 429-442.  
17925389 W.W.Ho, H.Li, S.Eakanunkul, Y.Tong, A.Wilks, M.Guo, and T.L.Poulos (2007).
Holo- and apo-bound structures of bacterial periplasmic heme-binding proteins.
  J Biol Chem, 282, 35796-35802.
PDB codes: 2r79 2r7a 2rg7
17171660 Z.G.Wang, B.B.Ke, and Z.K.Xu (2007).
Covalent immobilization of redox enzyme on electrospun nonwoven poly(acrylonitrile-co-acrylic acid) nanofiber mesh filled with carbon nanotubes: a comprehensive study.
  Biotechnol Bioeng, 97, 708-720.  
16879643 G.Wang, P.Alamuri, and R.J.Maier (2006).
The diverse antioxidant systems of Helicobacter pylori.
  Mol Microbiol, 61, 847-860.  
16609813 M.S.Lorentzen, E.Moe, H.M.Jouve, and N.P.Willassen (2006).
Cold adapted features of Vibrio salmonicida catalase: characterisation and comparison to the mesophilic counterpart from Proteus mirabilis.
  Extremophiles, 10, 427-440.  
16079130 A.M.Vetrano, D.E.Heck, T.M.Mariano, V.Mishin, D.L.Laskin, and J.D.Laskin (2005).
Characterization of the oxidase activity in mammalian catalase.
  J Biol Chem, 280, 35372-35381.  
15596434 K.Kobayashi, S.Yoshioka, Y.Kato, Y.Asano, and S.Aono (2005).
Regulation of aldoxime dehydratase activity by redox-dependent change in the coordination structure of the aldoxime-heme complex.
  J Biol Chem, 280, 5486-5490.  
15456778 G.Wang, R.C.Conover, S.Benoit, A.A.Olczak, J.W.Olson, M.K.Johnson, and R.J.Maier (2004).
Role of a bacterial organic hydroperoxide detoxification system in preventing catalase inactivation.
  J Biol Chem, 279, 51908-51914.  
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.