spacer
spacer

PDBsum entry 8cat

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
8cat
Jmol
Contents
Protein chains
498 a.a. *
Ligands
HEM ×2
NDP ×2
Waters ×98
* Residue conservation analysis
PDB id:
8cat
Name: Oxidoreductase
Title: The NADPH binding site on beef liver catalase
Structure: Catalase. Chain: a, b. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.191    
Authors: M.R.N.Murthy,T.J.Reid Iii,A.Sicignano,N.Tanaka,I.Fita,M.G.Ro
Key ref: I.Fita and M.G.Rossmann (1985). The NADPH binding site on beef liver catalase. Proc Natl Acad Sci U S A, 82, 1604-1608. PubMed id: 3856839 DOI: 10.1073/pnas.82.6.1604
Date:
15-Nov-84     Release date:   01-Apr-85    
Supersedes: 3cat
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00432  (CATA_BOVIN) -  Catalase
Seq:
Struc:
 
Seq:
Struc:
527 a.a.
498 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* 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; 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     membrane   6 terms 
  Biological process     oxidation-reduction process   17 terms 
  Biochemical function     antioxidant activity     12 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.82.6.1604 Proc Natl Acad Sci U S A 82:1604-1608 (1985)
PubMed id: 3856839  
 
 
The NADPH binding site on beef liver catalase.
I.Fita, M.G.Rossmann.
 
  ABSTRACT  
 
Beef liver and human erythrocyte catalases (EC 1.11.1.6) bind NADP tenaciously [Kirkman, H. N. & Gaetani, G. F. (1984) Proc. Natl. Acad. Sci. USA 81, 4343-4348]. The position of NADP on beef liver catalase corresponds to the carboxyl-terminal polypeptide hinge in Penicillium vitale fungal catalase, which connects the common catalase structure to the additional flavodoxin-like domain. In contrast to nearly all other known structures of protein-bound NADP, NAD, and FAD, the NADP molecule of beef liver catalase is folded into a right-handed helix and bound, in part, in the vicinity of the carboxyl end of two alpha-helices. A water molecule (W7) occupies a pseudosubstrate site close to the C4 position of the nicotinamide and is hydrogen bonded to His-304. Although the NADP and heme groups approach each other to within 13.7 A, there is no direct interaction. The function of the NADP remains a mystery.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21541840 B.Paital, S.Kumar, R.Farmer, N.K.Tripathy, and G.B.Chainy (2011).
In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata.
  Interdiscip Sci, 3, 110-120.  
  21077118 H.W.Zeng, Y.J.Cai, X.R.Liao, F.Zhang, and D.B.Zhang (2011).
Production, characterization, cloning and sequence analysis of a monofunctional catalase from Serratia marcescens SYBC08.
  J Basic Microbiol, 51, 205-214.  
20716293 D.E.Heck, M.Shakarjian, H.D.Kim, J.D.Laskin, and A.M.Vetrano (2010).
Mechanisms of oxidant generation by catalase.
  Ann N Y Acad Sci, 1203, 120-125.  
17158050 H.N.Kirkman, and G.F.Gaetani (2007).
Mammalian catalase: a venerable enzyme with new mysteries.
  Trends Biochem Sci, 32, 44-50.  
17456740 J.A.Knappenberger, and J.T.Lecomte (2007).
Loop anchor modification causes the population of an alternative native state in an SH3-like domain.
  Protein Sci, 16, 863-879.  
17183702 I.L.Calderón, F.A.Arenas, J.M.Pérez, D.E.Fuentes, M.A.Araya, C.P.Saavedra, J.C.Tantaleán, S.E.Pichuantes, P.A.Youderian, and C.C.Vásquez (2006).
Catalases are NAD(P)H-dependent tellurite reductases.
  PLoS ONE, 1, e70.  
17108904 N.C.Gibbons, J.M.Wood, H.Rokos, and K.U.Schallreuter (2006).
Computer simulation of native epidermal enzyme structures in the presence and absence of hydrogen peroxide (H2O2): potential and pitfalls.
  J Invest Dermatol, 126, 2576-2582.  
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.  
15760048 S.Giovagnoli, P.Blasi, M.Ricci, and C.Rossi (2004).
Biodegradable microspheres as carriers for native superoxide dismutase and catalase delivery.
  AAPS PharmSciTech, 5, e51.  
  12435514 C.Barrière, R.Brückner, D.Centeno, and R.Talon (2002).
Characterisation of the katA gene encoding a catalase and evidence for at least a second catalase activity in Staphylococcus xylosus, bacteria used in food fermentation.
  FEMS Microbiol Lett, 216, 277-283.  
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
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.  
11137458 K.Nakamura, M.Watanabe, K.Takanaka, Y.Sasaki, and T.Ikeda (2000).
cDNA cloning of mutant catalase in acatalasemic beagle dog: single nucleotide substitution leading to thermal-instability and enhanced proteolysis of mutant enzyme.
  Int J Biochem Cell Biol, 32, 1183-1193.  
  10477311 A.Marais, G.L.Mendz, S.L.Hazell, and F.Mégraud (1999).
Metabolism and genetics of Helicobacter pylori: the genome era.
  Microbiol Mol Biol Rev, 63, 642-674.  
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.  
  10493573 J.J.Tanner, S.C.Tu, L.J.Barbour, C.L.Barnes, and K.L.Krause (1999).
Unusual folded conformation of nicotinamide adenine dinucleotide bound to flavin reductase P.
  Protein Sci, 8, 1725-1732.
PDB code: 2bkj
10209276 M.Ghadermarzi, and A.A.Moosavi-Movahedi (1999).
Influence of different types of effectors on the kinetic parameters of suicide inactivation of catalase by hydrogen peroxide.
  Biochim Biophys Acta, 1431, 30-36.  
10216308 M.J.Maté, M.Ortiz-Lombardía, A.Marina, and I.Fita (1999).
Crystallization and preliminary structural results of catalase from human erythrocytes.
  Acta Crystallogr D Biol Crystallogr, 55, 1066-1068.  
  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.  
9586811 F.Hoffschir, L.Daya-Grosjean, P.X.Petit, S.Nocentini, B.Dutrillaux, A.Sarasin, and M.Vuillaume (1998).
Low catalase activity in xeroderma pigmentosum fibroblasts and SV40-transformed human cell lines is directly related to decreased intracellular levels of the cofactor, NADPH.
  Free Radic Biol Med, 24, 809-816.  
  9336832 C.E.Bell, T.O.Yeates, and D.Eisenberg (1997).
Unusual conformation of nicotinamide adenine dinucleotide (NAD) bound to diphtheria toxin: a comparison with NAD bound to the oxidoreductase enzymes.
  Protein Sci, 6, 2084-2096.  
  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.  
7786407 A.Buzy, V.Bracchi, R.Sterjiades, J.Chroboczek, P.Thibault, J.Gagnon, H.M.Jouve, and G.Hudry-Clergeon (1995).
Complete amino acid sequence of Proteus mirabilis PR catalase. Occurrence of a methionine sulfone in the close proximity of the active site.
  J Protein Chem, 14, 59-72.  
  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.  
7711270 P.Du, and G.H.Loew (1995).
Theoretical study of model compound I complexes of horseradish peroxidase and catalase.
  Biophys J, 68, 69-80.  
  7756992 L.E.Donate, E.Gherardi, N.Srinivasan, R.Sowdhamini, S.Aparicio, and T.L.Blundell (1994).
Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP).
  Protein Sci, 3, 2378-2394.  
7922042 M.J.Adams, G.H.Ellis, S.Gover, C.E.Naylor, and C.Phillips (1994).
Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism.
  Structure, 2, 651-668.
PDB codes: 1pgn 1pgo 1pgp 1pgq
  8003987 T.Kitlar, F.Döring, D.F.Diedrich, R.Frank, H.Wallmeier, R.K.Kinne, and J.Deutscher (1994).
Interaction of phlorizin, a potent inhibitor of the Na+/D-glucose cotransporter, with the NADPH-binding site of mammalian catalases.
  Protein Sci, 3, 696-700.  
  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.  
1459249 A.Hillar, and P.Nicholls (1992).
A mechanism for NADPH inhibition of catalase compound II formation.
  FEBS Lett, 314, 179-182.  
1591412 T.Furuno, K.M.Ulmer, and H.Sasabe (1992).
Scanning electron microscopy of negatively stained catalase on a silicon wafer.
  Microsc Res Tech, 21, 32-38.  
  1987146 I.von Ossowski, M.R.Mulvey, P.A.Leco, A.Borys, and P.C.Loewen (1991).
Nucleotide sequence of Escherichia coli katE, which encodes catalase HPII.
  J Bacteriol, 173, 514-520.  
1846966 M.L.Smith, J.Paul, P.I.Ohlsson, K.Hjortsberg, and K.G.Paul (1991).
Heme-protein fission under nondenaturing conditions.
  Proc Natl Acad Sci U S A, 88, 882-886.  
2682654 J.H.Hurley, P.E.Thorsness, V.Ramalingam, N.H.Helmers, D.E.Koshland, and R.M.Stroud (1989).
Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase.
  Proc Natl Acad Sci U S A, 86, 8635-8639.
PDB code: 3icd
2775840 N.Ramasubbu, and R.Parthasarathy (1989).
Role of water molecules in the crystal structure of Gly-L-Ala-L-Phe: a possible sequence preference for nucleation of alpha-helix?
  Biopolymers, 28, 1259-1269.  
2771946 S.R.Presnell, and F.E.Cohen (1989).
Topological distribution of four-alpha-helix bundles.
  Proc Natl Acad Sci U S A, 86, 6592-6596.  
3046940 G.Cohen, W.Rapatz, and H.Ruis (1988).
Sequence of the Saccharomyces cerevisiae CTA1 gene and amino acid sequence of catalase A derived from it.
  Eur J Biochem, 176, 159-163.  
3691514 H.Okada, M.Ueda, T.Sugaya, H.Atomi, S.Mozaffar, T.Hishida, Y.Teranishi, K.Okazaki, T.Takechi, and T.Kamiryo (1987).
Catalase gene of the yeast Candida tropicalis. Sequence analysis and comparison with peroxisomal and cytosolic catalases from other sources.
  Eur J Biochem, 170, 105-110.  
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 code is shown on the right.