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Oxidoreductase PDB id
1hbz
Jmol
Contents
Protein chain
498 a.a. *
Ligands
HEM
SO4
Waters ×538
* Residue conservation analysis
PDB id:
1hbz
Name: Oxidoreductase
Title: Catalase from micrococcus lysodeikticu
Structure: Catalase. Chain: a. Ec: 1.11.1.6
Source: Micrococcus lysodeikticus. Organism_taxid: 1270
Biol. unit: Tetramer (from PDB file)
Resolution:
1.5Å     R-factor:   0.092     R-free:   0.120
Authors: G.N.Murshudov,A.I.Grebenko,V.V.Barynin,J.Braningen, K.S.Wilson,Z.Dauter,W.R.Melik-Adamyan
Key ref: G.N.Murshudov et al. (1992). Three-dimensional structure of catalase from Micrococcus lysodeikticus at 1.5 A resolution. FEBS Lett, 312, 127-131. PubMed id: 1426241 DOI: 10.1016/0014-5793(92)80919-8
Date:
24-Apr-01     Release date:   24-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29422  (CATA_MICLU) -  Catalase
Seq:
Struc: 		503 a.a.
498 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 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; Manganese
Heme
Bound ligand (Het Group name = HEM) matches with 95.00% similarity 		Manganese
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   3 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0014-5793(92)80919-8 FEBS Lett 312:127-131 (1992)
PubMed id: 1426241  
 
 
Three-dimensional structure of catalase from Micrococcus lysodeikticus at 1.5 A resolution.
G.N.Murshudov, W.R.Melik-Adamyan, A.I.Grebenko, V.V.Barynin, A.A.Vagin, B.K.Vainshtein, Z.Dauter, K.S.Wilson.
 
  ABSTRACT  
 
The three-dimensional crystal structure of catalase from Micrococcus lysodeikticus has been solved by multiple isomorphous replacement and refined at 1.5 A resolution. The subunit of the tetrameric molecule of 222 symmetry consists of a single polypeptide chain of about 500 amino acid residues and one haem group. The crystals belong to space group P4(2)2(1)2 with unit cell parameters a = b = 106.7 A, c = 106.3 A, and there is one subunit of the tetramer per asymmetric unit. The amino acid sequence has been tentatively determined by computer graphics model building and comparison with the known three-dimensional structure of beef liver catalase and sequences of several other catalases. The atomic model has been refined by Hendrickson and Konnert's least-squares minimisation against 94,315 reflections between 8 A and 1.5 A. The final model consists of 3,977 non-hydrogen atoms of the protein and haem group, 426 water molecules and one sulphate ion. The secondary and tertiary structures of the bacterial catalase have been analyzed and a comparison with the structure of beef liver catalase has been made.
 

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
18498226 M.Zamocky, P.G.Furtmüller, and C.Obinger (2008).
Evolution of catalases from bacteria to humans.
  Antioxid Redox Signal, 10, 1527-1548.  
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.  
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
14646074 P.Andreoletti, A.Pernoud, G.Sainz, P.Gouet, and H.M.Jouve (2003).
Structural studies of Proteus mirabilis catalase in its ground state, oxidized state and in complex with formic acid.
  Acta Crystallogr D Biol Crystallogr, 59, 2163-2168.
PDB codes: 1mqf 1nm0
12486720 P.Andreoletti, G.Sainz, M.Jaquinod, J.Gagnon, and H.M.Jouve (2003).
High-resolution structure and biochemical properties of a recombinant Proteus mirabilis catalase depleted in iron.
  Proteins, 50, 261-271.
PDB codes: 1e93 1h6n
12557185 X.Carpena, M.Soriano, M.G.Klotz, H.W.Duckworth, L.J.Donald, W.Melik-Adamyan, I.Fita, and P.C.Loewen (2003).
Structure of the Clade 1 catalase, CatF of Pseudomonas syringae, at 1.8 A resolution.
  Proteins, 50, 423-436.
PDB code: 1m7s
12454454 G.N.Murshudov, A.I.Grebenko, J.A.Brannigan, A.A.Antson, V.V.Barynin, G.G.Dodson, Z.Dauter, K.S.Wilson, and W.R.Melik-Adamyan (2002).
The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex.
  Acta Crystallogr D Biol Crystallogr, 58, 1972-1982.
PDB codes: 1gwe 1gwf 1gwh
11455600 W.Melik-Adamyan, J.Bravo, X.Carpena, J.Switala, M.J.Maté, I.Fita, and P.C.Loewen (2001).
Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli.
  Proteins, 44, 270-281.
PDB codes: 1gg9 1gge 1ggf 1ggh 1ggj 1ggk
11468413 X.Carpena, R.Perez, W.F.Ochoa, N.Verdaguer, M.G.Klotz, J.Switala, W.Melik-Adamyan, I.Fita, and P.C.Loewen (2001).
Crystallization and preliminary X-ray analysis of clade I catalases from Pseudomonas syringae and Listeria seeligeri.
  Acta Crystallogr D Biol Crystallogr, 57, 1184-1186.  
10089417 G.N.Murshudov, A.A.Vagin, A.Lebedev, K.S.Wilson, and E.J.Dodson (1999).
Efficient anisotropic refinement of macromolecular structures using FFT.
  Acta Crystallogr D Biol Crystallogr, 55, 247-255.  
10488114 M.J.Maté, M.S.Sevinc, B.Hu, J.Bujons, J.Bravo, J.Switala, W.Ens, P.C.Loewen, and I.Fita (1999).
Mutants that alter the covalent structure of catalase hydroperoxidase II from Escherichia coli.
  J Biol Chem, 274, 27717-27725.
PDB codes: 1cf9 1qf7
  10091651 M.S.Sevinc, M.J.Maté, J.Switala, I.Fita, and P.C.Loewen (1999).
Role of the lateral channel in catalase HPII of Escherichia coli.
  Protein Sci, 8, 490-498.  
10417406 T.P.Ko, J.Day, A.J.Malkin, and A.McPherson (1999).
Structure of orthorhombic crystals of beef liver catalase.
  Acta Crystallogr D Biol Crystallogr, 55, 1383-1394.
PDB code: 4blc
  9144772 J.Bravo, I.Fita, J.C.Ferrer, W.Ens, A.Hillar, J.Switala, and P.C.Loewen (1997).
Identification of a novel bond between a histidine and the essential tyrosine in catalase HPII of Escherichia coli.
  Protein Sci, 6, 1016-1023.  
  9083108 M.Bergdoll, M.H.Remy, C.Cagnon, J.M.Masson, and P.Dumas (1997).
Proline-dependent oligomerization with arm exchange.
  Structure, 5, 391-401.  
  9041655 S.Berthet, L.M.Nykyri, J.Bravo, M.J.Mate, C.Berthet-Colominas, P.M.Alzari, F.Koller, and I.Fita (1997).
Crystallization and preliminary structural analysis of catalase A from Saccharomyces cerevisiae.
  Protein Sci, 6, 481-483.  
  8955300 D.Hérouart, S.Sigaud, S.Moreau, P.Frendo, D.Touati, and A.Puppo (1996).
Cloning and characterization of the katA gene of Rhizobium meliloti encoding a hydrogen peroxide-inducible catalase.
  J Bacteriol, 178, 6802-6809.  
8621527 G.N.Murshudov, A.I.Grebenko, V.Barynin, Z.Dauter, K.S.Wilson, B.K.Vainshtein, W.Melik-Adamyan, J.Bravo, J.M.Ferrán, J.C.Ferrer, J.Switala, P.C.Loewen, and I.Fita (1996).
Structure of the heme d of Penicillium vitale and Escherichia coli catalases.
  J Biol Chem, 271, 8863-8868.  
8901874 P.Gouet, H.M.Jouve, P.A.Williams, I.Andersson, P.Andreoletti, L.Nussaume, and J.Hajdu (1996).
Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy.
  Nat Struct Biol, 3, 951-956.
PDB codes: 2caf 2cag
  7768808 E.R.Rocha, and C.J.Smith (1995).
Biochemical and genetic analyses of a catalase from the anaerobic bacterium Bacteroides fragilis.
  J Bacteriol, 177, 3111-3119.  
7737979 J.al-Mustafa, M.Sykora, and J.R.Kincaid (1995).
Resonance Raman investigation of cyanide ligated beef liver and Aspergillus niger catalases.
  J Biol Chem, 270, 10449-10460.  
7546603 M.G.Klotz, Y.C.Kim, J.Katsuwon, and A.J.Anderson (1995).
Cloning, characterization and phenotypic expression in Escherichia coli of catF, which encodes the catalytic subunit of catalase isozyme CatF of Pseudomonas syringae.
  Appl Microbiol Biotechnol, 43, 656-666.  
  8188593 W.R.Bishai, H.O.Smith, and G.J.Barcak (1994).
A peroxide/ascorbate-inducible catalase from Haemophilus influenzae is homologous to the Escherichia coli katE gene product.
  J Bacteriol, 176, 2914-2921.  
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.