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PDBsum entry 4cat

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Oxidoreductase(h2o2(a)) PDB id
4cat
Jmol
Contents
Protein chains
659 a.a.
Ligands
HEM ×2
PDB id:
4cat
Name: Oxidoreductase(h2o2(a))
Title: Three-dimensional structure of catalase from penicillium vit angstroms resolution
Structure: Catalase. Chain: a, b. Engineered: yes
Source: Penicillium janthinellum. Organism_taxid: 5079
Biol. unit: Tetramer (from PQS)
Resolution:
3.00Å     R-factor:   not given    
Authors: B.K.Vainshtein,W.R.Melik-Adamyan,V.V.Barynin,A.A.Vagin,A.I.G
Key ref:
B.K.Vainshtein et al. (1986). Three-dimensional structure of catalase from Penicillium vitale at 2.0 A resolution. J Mol Biol, 188, 49-61. PubMed id: 3712443 DOI: 10.1016/0022-2836(86)90479-1
Date:
24-Feb-83     Release date:   06-Sep-83    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc:  
Struc: 659 a.a.
Key:    Secondary structure

 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 95.45% similarity
Manganese
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/0022-2836(86)90479-1 J Mol Biol 188:49-61 (1986)
PubMed id: 3712443  
 
 
Three-dimensional structure of catalase from Penicillium vitale at 2.0 A resolution.
B.K.Vainshtein, W.R.Melik-Adamyan, V.V.Barynin, A.A.Vagin, A.I.Grebenko, V.V.Borisov, K.S.Bartels, I.Fita, M.G.Rossmann.
 
  ABSTRACT  
 
The three-dimensional structure analysis of crystalline fungal catalase from Penicillium vitale has been extended to 2.0 A resolution. The crystals belong to space group P3(1)21, with the unit cell parameters of a = b = 144.4 A and c = 133.8 A. The asymmetric unit contains half a tetrameric molecule of 222 symmetry. Each subunit is a single polypeptide chain of approximately 670 amino acid residues and binds one heme group. The amino acid sequence has been tentatively determined by computer graphics model building (using the FRODO system) and comparison with the known sequence of beef liver catalase. The atomic model has been refined by the Hendrickson & Konnert (1981) restrained least-squares program against 68,000 reflections between 5 A and 2 A resolution. The final R-factor is 0.31 after 24 refinement cycles. The secondary and tertiary structure of the catalase has been analyzed.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. ependence f the rystallographic R-factor on the reciprocal of resolution. Theoretical distributions are for ean o-ordinate errors between 0.3 ad 0.5 x. as desrribed by uzzati 1952).
Figure 8.
Figure 8. Strreo iew f the elecron ensity Ed motkl in he Iwrnt~ .icinitJ
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1986, 188, 49-61) copyright 1986.  
  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
18369615 D.Sutay Kocabas, U.Bakir, S.E.Phillips, M.J.McPherson, and Z.B.Ogel (2008).
Purification, characterization, and identification of a novel bifunctional catalase-phenol oxidase from Scytalidium thermophilum.
  Appl Microbiol Biotechnol, 79, 407-415.  
18498226 M.Zamocky, P.G.Furtmüller, and C.Obinger (2008).
Evolution of catalases from bacteria to humans.
  Antioxid Redox Signal, 10, 1527-1548.  
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
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
11728803 A.Díaz, P.Rangel, Y.Montes de Oca, F.Lledías, and W.Hansberg (2001).
Molecular and kinetic study of catalase-1, a durable large catalase of Neurospora crassa.
  Free Radic Biol Med, 31, 1323-1333.  
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.  
10022351 J.Bravo, M.J.Mate, T.Schneider, J.Switala, K.Wilson, P.C.Loewen, and I.Fita (1999).
Structure of catalase HPII from Escherichia coli at 1.9 A resolution.
  Proteins, 34, 155-166.  
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
9553125 F.Lledías, P.Rangel, and W.Hansberg (1998).
Oxidation of catalase by singlet oxygen.
  J Biol Chem, 273, 10630-10637.  
  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.  
  9150225 L.Kawasaki, D.Wysong, R.Diamond, and J.Aguirre (1997).
Two divergent catalase genes are differentially regulated during Aspergillus nidulans development and oxidative stress.
  J Bacteriol, 179, 3284-3292.  
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.  
9144791 W.A.Shirley, and C.L.Brooks (1997).
Curious structure in "canonical" alanine-based peptides.
  Proteins, 28, 59-71.  
  8844857 C.A.Rohl, and A.J.Doig (1996).
Models for the 3(10)-helix/coil, pi-helix/coil, and alpha-helix/3(10)-helix/coil transitions in isolated peptides.
  Protein Sci, 5, 1687-1696.  
  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.  
  8732765 K.R.Rajashankar, and S.Ramakumar (1996).
Pi-turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence.
  Protein Sci, 5, 932-946.  
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.  
  8143488 M.S.Johnson, N.Srinivasan, R.Sowdhamini, and T.L.Blundell (1994).
Knowledge-based protein modeling.
  Crit Rev Biochem Mol Biol, 29, 1.  
  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.  
8425895 F.Kragler, A.Langeder, J.Raupachova, M.Binder, and A.Hartig (1993).
Two independent peroxisomal targeting signals in catalase A of Saccharomyces cerevisiae.
  J Cell Biol, 120, 665-673.  
7934925 T.Fowler, M.W.Rey, P.Vähä-Vahe, S.D.Power, and R.M.Berka (1993).
The catR gene encoding a catalase from Aspergillus niger: primary structure and elevated expression through increased gene copy number and use of a strong promoter.
  Mol Microbiol, 9, 989-998.  
1468561 S.Hu, and J.R.Kincaid (1992).
Resonance Raman studies of the carbonmonoxy form of catalase. Evidence for and effects of phenolate ligation.
  FEBS Lett, 314, 293-296.  
  3259176 J.P.Priestle, H.P.Schär, and M.G.Grütter (1988).
Crystal structure of the cytokine interleukin-1 beta.
  EMBO J, 7, 339-343.  
3322951 H.B.Dunford (1987).
Free radicals in iron-containing systems.
  Free Radic Biol Med, 3, 405-421.  
3536508 A.Hartig, and H.Ruis (1986).
Nucleotide sequence of the Saccharomyces cerevisiae CTT1 gene and deduced amino-acid sequence of yeast catalase T.
  Eur J Biochem, 160, 487-490.  
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.