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PDBsum entry 1a4e

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1a4e
Jmol
Contents
Protein chains
488 a.a. *
Ligands
AZI ×2
SO4 ×2
HEM ×2
AZI-HEM ×2
Waters ×957
* Residue conservation analysis
PDB id:
1a4e
Name: Oxidoreductase
Title: Catalase a from saccharomyces cerevisiae
Structure: Catalase a. Chain: a, b, c, d. Ec: 1.11.1.6
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Cellular_location: peroxisomes
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
2.40Å     R-factor:   0.154     R-free:   0.198
Authors: M.J.Mate
Key ref:
M.J.Maté et al. (1999). Structure of catalase-A from Saccharomyces cerevisiae. J Mol Biol, 286, 135-149. PubMed id: 9931255 DOI: 10.1006/jmbi.1998.2453
Date:
29-Jan-98     Release date:   13-Aug-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P15202  (CATA_YEAST) -  Peroxisomal catalase A
Seq:
Struc:
515 a.a.
488 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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     peroxisome   3 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     protein binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1998.2453 J Mol Biol 286:135-149 (1999)
PubMed id: 9931255  
 
 
Structure of catalase-A from Saccharomyces cerevisiae.
M.J.Maté, M.Zamocky, L.M.Nykyri, C.Herzog, P.M.Alzari, C.Betzel, F.Koller, I.Fita.
 
  ABSTRACT  
 
The structure of the peroxisomal catalase A from the budding yeast Saccharomyces cerevisiae, with 515 residues per subunit, has been determined and refined to 2.4 A resolution. The crystallographic agreement factors R and Rfree are 15.4% and 19.8%, respectively. A tetramer with accurate 222-molecular symmetry is located in the asymmetric unit of the crystal. The conformation of the central core of catalase A, about 300 residues, remains similar to the structure of catalases from distantly related organisms. In contrast, catalase A lacks a carboxy-terminal domain equivalent to that found in catalase from Penicillium vitalae, the only other fungal catalase structure available. Structural peculiarities related with the heme and NADP(H) binding pockets can be correlated with biochemical characteristics of the catalase A enzyme. The network of molecular cavities and channels, filled with solvent molecules, supports the existence of one major substrate entry and at least two possible alternative pathways to the heme active site. The structure of the variant protein Val111Ala, also determined by X-ray crystallography at 2.8 A resolution, shows a few, well-localized, differences with respect to the wild-type enzyme. These differences, that include the widening of the entry channel in its narrowest point, provide an explanation for both the increased peroxidatic activity and the reduced catalatic activity of this mutant.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Stereo views of the heme group environment in SCC-A. (a) side heme view and (b) view perpendicular to the heme plane. Carbon, oxygen and nitrogen atoms are represented as open, shaded and filled spheres, respectively. Hydrogen bonds are indicated by broken lines. The heme group, the azide molecule found in the distal side, the essential catalytic residues (His70, Ser109, Asn143, Arg351 and Tyr355), and two water molecules which are hydrogen-bonded to the propionic groups are explicitly shown in (a). The deprotonated oxygen of Tyr355, that makes two ionic hydrogen bonds with Arg351, acts as the proximal ligand of the iron atom (coordination is also indicated with a discontinuous bond). Residues that define the heme distal pocket are explicitly shown in (b). Asn68 interacts with Asp62 from the R related subunit (indicated by the symbol * in the Figure) and with a solvent molecule which starts a chain of water molecules that reach the central cavity of the catalase molecules (see the text). Neither the main-chain oxygen atom of cis-Pro69 nor the side-chain oxygen atom of Asn143 form standard hydrogen bonds and might interact with the heme ring.
Figure 7.
Figure 7. Stereo view of the final (2F[o] - F[c]) electron density map showing the network of bonds that bridge the two pairs of heme groups in an SCC-A molecule (see the text and [Gouet et al 1995]). Heme groups and residues Asn60, Arg61, Asp357, together with four water molecules and two sulphate ions are also shown inside the density. The four subunits participate in each one of these heme-heme connections. Density for the azide molecules, situated in the heme distal pockets and coordinated with the iron atoms, can also be seen in this drawing. Sulfate ions are located on the molecular 2-fold axis P. The quality of the electron density allows to define unambiguously the hand of the heme group from the disposition of methyl and vinyl groups. For clarity only density situated till about 2.5 Å from the atoms represented is shown.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 286, 135-149) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19715615 M.I.González-Siso, A.García-Leiro, N.Tarrío, and M.E.Cerdán (2009).
Sugar metabolism, redox balance and oxidative stress response in the respiratory yeast Kluyveromyces lactis.
  Microb Cell Fact, 8, 46.  
18498226 M.Zamocky, P.G.Furtmüller, and C.Obinger (2008).
Evolution of catalases from bacteria to humans.
  Antioxid Redox Signal, 10, 1527-1548.  
17046020 I.M.Moustafa, S.Foster, A.Y.Lyubimov, and A.Vrielink (2006).
Crystal structure of LAAO from Calloselasma rhodostoma with an L-phenylalanine substrate: insights into structure and mechanism.
  J Mol Biol, 364, 991.
PDB code: 2iid
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.  
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.  
16244360 C.Jakopitsch, E.Droghetti, F.Schmuckenschlager, P.G.Furtmüller, G.Smulevich, and C.Obinger (2005).
Role of the main access channel of catalase-peroxidase in catalysis.
  J Biol Chem, 280, 42411-42422.  
16217656 C.Mandal, R.D.Gudi, and G.K.Suraishkumar (2005).
Multi-objective optimization in Aspergillus niger fermentation for selective product enhancement.
  Bioprocess Biosyst Eng, 28, 149-164.  
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
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
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
11134921 M.K.Safo, F.N.Musayev, S.H.Wu, D.J.Abraham, and T.P.Ko (2001).
Structure of tetragonal crystals of human erythrocyte catalase.
  Acta Crystallogr D Biol Crystallogr, 57, 1-7.
PDB code: 1f4j
11506915 P.H.Goodwin, J.Li, and S.Jin (2001).
A catalase gene of Colletotrichum gloeosporioides f. sp. malvae is highly expressed during the necrotrophic phase of infection of round-leaved mallow, Malva pusilla.
  FEMS Microbiol Lett, 202, 103-107.  
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.  
10666617 T.P.Ko, M.K.Safo, F.N.Musayev, M.L.Di Salvo, C.Wang, S.H.Wu, and D.J.Abraham (2000).
Structure of human erythrocyte catalase.
  Acta Crystallogr D Biol Crystallogr, 56, 241-245.
PDB code: 1qqw
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
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.