PDBsum entry: 1iph

Oxidoreductase

PDB id: 1iph

Contents

Protein chains

727 a.a. *

Ligands

HEM ×4

* Residue conservation analysis

PDB id:

1iph

Name:

Oxidoreductase

Title:

Structure of catalase hpii from escherichia coli

Structure:

Catalase hpii. Chain: a, b, c, d. Ec: 1.11.1.6

Source:

Escherichia coli. Organism_taxid: 562. Organ: liver

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.200

Authors:

J.Bravo,P.C.Loewen,I.Fita

Key ref:

J.Bravo et al. (1995). Crystal structure of catalase HPII from Escherichia coli. Structure, 3, 491-502. PubMed id: 7663946 DOI: 10.1016/S0969-2126(01)00182-4

Date:

31-Dec-95 Release date: 04-Sep-97

Protein chains

P21179  (CATE_ECOLI) -  Catalase HPII

Seq: 753 a.a.

Struc: 727 a.a.

Enzyme reactions

• Enzyme class: E.C.1.11.1.6 - Catalase.
• Reaction: 2 H₂O₂ = O₂ + 2 H₂O
• 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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: oxidoreductase activity (6 terms)

reference

DOI no: 10.1016/S0969-2126(01)00182-4

Structure 3:491-502 (1995)

PubMed id: 7663946

Crystal structure of catalase HPII from Escherichia coli.

J.Bravo, N.Verdaguer, J.Tormo, C.Betzel, J.Switala, P.C.Loewen, I.Fita.

ABSTRACT

BACKGROUND: Catalase is a ubiquitous enzyme present in both the prokaryotic and eukaryotic cells of aerobic organisms. It serves, in part, to protect the cell from the toxic effects of small peroxides. Escherichia coli produces two catalases, HPI and HPII, that are quite distinct from other catalases in physical structure and catalytic properties. HPII, studied in this work, is encoded by the katE gene, and has been characterized as an oligomeric, monofunctional catalase containing one cis-heme d prosthetic group per subunit of 753 residues. RESULTS: The crystal structure of catalase HPII from E. coli has been determined to 2.8 A resolution. The asymmetric unit of the crystal contains a whole molecule, which is a tetramer with accurate 222 point group symmetry. In the model built, that includes residues 27-753 and one heme group per monomer, strict non-crystallographic symmetry has been maintained. The crystallographic agreement R-factor is 20.1% for 58,477 reflections in the resolution shell 8.0-2.8 A. CONCLUSIONS: Despite differences in size and chemical properties, which were suggestive of a unique catalase, the deduced structure of HPII is related to the structure of catalase from Penicillium vitale, whose sequence is not yet known. In particular, both molecules have an additional C-terminal domain that is absent in the bovine catalase. This extra domain contains a Rossmann fold but no bound nucleotides have been detected, and its physiological role is unknown. In HPII, the heme group is modified to a heme d and inverted with respect to the orientation determined in all previously reported heme catalases. HPII is the largest catalase for which the structure has been determined to almost atomic resolution.

Selected figure(s)

Figure 2.
Figure 2. Representative stereoviews of the final averaged (2F[o]–F[c]) electron-density map. Residues (a) Ile274 and (b) His739 are outside energetically favorable regions in the Ramachandran diagram (see Figure 3). The identification of the bulky residue Trp742 (b) facilitated the tracing of the C-terminal domain. (c) Exposed segment in the hinge region, including residues Pro575-Pro576-Pro577. Figure 2. Representative stereoviews of the final averaged (2F[o]–F[c]) electron-density map. Residues (a) Ile274 and (b) His739 are outside energetically favorable regions in the Ramachandran diagram (see [5]Figure 3). The identification of the bulky residue Trp742 (b) facilitated the tracing of the C-terminal domain. (c) Exposed segment in the hinge region, including residues Pro575-Pro576-Pro577.

Figure 10.
Figure 10. Stereoview of the electron density in the terminal carboxylate environment (residue Ala753). The molecular dyad R-axis-related residues are shown with thinner bonds. The terminal carboxylate charged group appears to be neutralized by Lys309. Figure 10. Stereoview of the electron density in the terminal carboxylate environment (residue Ala753). The molecular dyad R-axis-related residues are shown with thinner bonds. The terminal carboxylate charged group appears to be neutralized by Lys309.

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 491-502) copyright 1995.

Figures were selected by an automated process.