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PDBsum entry 1m7s

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Oxidoreductase PDB id
1m7s
Jmol
Contents
Protein chains
484 a.a. *
Ligands
HEM ×4
Waters ×2129
* Residue conservation analysis
PDB id:
1m7s
Name: Oxidoreductase
Title: Crystal structure analysis of catalase catf of pseudomonas syringae
Structure: Catalase. Chain: a, b, c, d. Engineered: yes
Source: Pseudomonas syringae. Organism_taxid: 317. Gene: catf. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.80Å     R-factor:   0.183     R-free:   0.240
Authors: X.Carpena,M.Soriano,M.G.Klotz,H.W.Duckworth,L.J.Donald, W.Melik-Adamyan,I.Fita,P.C.Loewen
Key ref:
X.Carpena et al. (2003). Structure of the Clade 1 catalase, CatF of Pseudomonas syringae, at 1.8 A resolution. Proteins, 50, 423-436. PubMed id: 12557185 DOI: 10.1002/prot.10284
Date:
22-Jul-02     Release date:   28-Aug-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P46206  (CATB_PSESY) -  Catalase
Seq:
Struc:
510 a.a.
484 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 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 95.00% similarity
Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.10284 Proteins 50:423-436 (2003)
PubMed id: 12557185  
 
 
Structure of the Clade 1 catalase, CatF of Pseudomonas syringae, at 1.8 A resolution.
X.Carpena, M.Soriano, M.G.Klotz, H.W.Duckworth, L.J.Donald, W.Melik-Adamyan, I.Fita, P.C.Loewen.
 
  ABSTRACT  
 
Catalase CatF of Pseudomonas syringae has been identified phylogenetically as a clade 1 catalase, closely related to plant catalases, a group from which no structure has been determined. The structure of CatF has been refined at 1.8 A resolution by using X-ray synchrotron data collected from a crystal flash-cooled with liquid nitrogen. The crystallographic agreement factors R and R(free) are, respectively, 18.3% and 24.0%. The asymmetric unit of the crystal contains a whole molecule that shows accurate 222-point group symmetry. The crystallized enzyme is a homotetramer of subunits with 484 residues, some 26 residues shorter than predicted from the DNA sequence. Mass spectrometry analysis confirmed the absence of 26 N-terminal residues, possibly removed by a periplasmic transport system. The core structure of the CatF subunit was closely related to seven other catalases with root-mean-square deviations (RMSDs) of 368 core Calpha atoms of 0.99-1.30 A. The heme component of CatF is heme b in the same orientation that is found in Escherichia coli hydroperoxidase II, an orientation that is flipped 180 degrees with respect the orientation of the heme in bovine liver catalase. NADPH is not found in the structure of CatF because key residues required for nucleotide binding are missing; 2129 water molecules were refined into the model. Water occupancy in the main or perpendicular channel of CatF varied among the four subunits from two to five in the region between the heme and the conserved Asp150. A comparison of the water occupancy in this region with the same region in other catalases reveals significant differences among the catalases.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Stereo views of CatF to illustrate the association of subunits. a: Subunit A is shown in blue. b: Subunits A and C (in red) associate so that their N-termini are overlapped by a loop on the opposite subunit. c: Subunits B (green) and D (yellow) have formed a similar intertwined dimmer, which is associated with the A-C dimer to form the tetramer.
Figure 6.
Figure 6. Stereo view of the heme orientation in HEC (a) and HPII (b). A stereo view of the F[o] - F[c] omit map of the heme pocket in subunit A of CatF generated without heme in the model during refinement is shown in red in (c). The heme is superimposed into the density to illustrate clearly the similarity to the orientation in HPII. The active site His and Asn are indicated. In HEC, the active site His is located above ring III of the heme (His-III orientation), and in HPII the active site His is located above ring IV of the heme (His-IV orientation). The axis of rotation, indicated in (c), is rotated slightly relative to the view in other figures.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2003, 50, 423-436) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.  
17080610 N.Engel, M.Schmidt, C.Lütz, and J.Feierabend (2006).
Molecular identification, heterologous expression and properties of light-insensitive plant catalases.
  Plant Cell Environ, 29, 593-607.  
16513636 T.Tosha, T.Uchida, A.R.Brash, and T.Kitagawa (2006).
On the relationship of coral allene oxide synthase to catalase. A single active site mutation that induces catalase activity in coral allene oxide synthase.
  J Biol Chem, 281, 12610-12617.  
15625113 M.L.Oldham, A.R.Brash, and M.E.Newcomer (2005).
The structure of coral allene oxide synthase reveals a catalase adapted for metabolism of a fatty acid hydroperoxide.
  Proc Natl Acad Sci U S A, 102, 297-302.
PDB code: 1u5u
15272159 K.O.Håkansson, M.Brugna, and L.Tasse (2004).
The three-dimensional structure of catalase from Enterococcus faecalis.
  Acta Crystallogr D Biol Crystallogr, 60, 1374-1380.
PDB code: 1si8
12777389 P.Chelikani, X.Carpena, I.Fita, and P.C.Loewen (2003).
An electrical potential in the access channel of catalases enhances catalysis.
  J Biol Chem, 278, 31290-31296.
PDB codes: 1p7y 1p7z 1p80 1p81 1qws
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.