PDBsum entry 1gwh

Oxidoreductase

PDB id: 1gwh

Contents

Protein chain

498 a.a. *

Ligands

HEM

NDP-SO4

ACT ×2

Waters ×568

* Residue conservation analysis

PDB id:

1gwh

Name:

Oxidoreductase

Title:

Atomic resolution structure of micrococcus lysodeikticus catalase complexed with NADPH

Structure:

Catalase. Chain: a. Ec: 1.11.1.6

Source:

Micrococcus luteus. Micrococcus lysodeikticus. Organism_taxid: 1270

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.74Å R-factor: 0.111 R-free: 0.138

Authors:

G.N.Murshudov,A.I.Grebenko,J.A.Brannigan,A.A.Antson,V.V.Barynin, G.G.Dodson,Z.Dauter,K.S.Wilson,W.R.Melik-Adamyan

Key ref:

G.N.Murshudov et al. (2002). The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex. Acta Crystallogr D Biol Crystallogr, 58, 1972-1982. PubMed id: 12454454 DOI: 10.1107/S0907444902016566

Date:

15-Mar-02 Release date: 19-Mar-02

Protein chain

P29422  (CATA_MICLU) -  Catalase from Micrococcus luteus

Seq: 503 a.a.

Struc: 498 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

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

reference

DOI no: 10.1107/S0907444902016566

Acta Crystallogr D Biol Crystallogr 58:1972-1982 (2002)

PubMed id: 12454454

The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex.

G.N.Murshudov, A.I.Grebenko, J.A.Brannigan, A.A.Antson, V.V.Barynin, G.G.Dodson, Z.Dauter, K.S.Wilson, W.R.Melik-Adamyan.

ABSTRACT

The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.

Selected figure(s)

Figure 1.
Figure 1 Stereoview of (a) ribbon diagram of the MLC tetramer and (b) CA trace of the M. lysodeikticus catalase monomer (in red) superimposed with that of beef liver catalase (in black). Figures were generated using MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).

Figure 6.
Figure 6 (a) Electron density demonstrating oxygen binding to the haem Fe atom (orange) in compound II. C atoms are coloured grey, O atoms red and N atoms blue. The final 2F[o] - F[c] map (contoured at 1 level) is in blue. (b) Comparison of the active site in resting MLC-0.88 (red) with MLC-PAA (blue).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1972-1982) copyright 2002.

Figures were selected by an automated process.