1GWH

Atomic resolution structure of Micrococcus Lysodeikticus catalase complexed with NADPH

Summary for 1GWH

• Entry DOI: 10.2210/pdb1gwh/pdb
• Related: 1GWE 1GWF
• Descriptor: Catalase, PROTOPORPHYRIN IX CONTAINING FE, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... (6 entities in total)
• Functional Keywords: oxidoreductase, catalase, hydrogen peroxide oxidoreductase, peroxidase
• Biological source: Micrococcus luteus (Micrococcus lysodeikticus)
• Total number of polymer chains: 1
• Total formula weight: 58538.63

Authors

Murshudov, G.N.,Grebenko, A.I.,Brannigan, J.A.,Antson, A.A.,Barynin, V.V.,Dodson, G.G.,Dauter, Z.,Wilson, K.S.,Melik-Adamyan, W.R. (deposition date: 2002-03-15, release date: 2002-03-19, Last modification date: 2024-05-08)

Primary citation

Murshudov, G.N.,Grebenko, A.I.,Brannigan, J.A.,Antson, A.A.,Barynin, V.V.,Dodson, G.G.,Dauter, Z.,Wilson, K.S.,Melik-Adamyan, W.R.
The Structures of Micrococcus Lysodeikticus Catalase, its Ferryl Intermediate (Compound II) and Nadph Complex.
Acta Crystallogr.,Sect.D, 58:1972-1982, 2002

PubMed 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.

PubMed: 12454454
DOI: 10.1107/S0907444902016566

Experimental method

X-RAY DIFFRACTION (1.74 Å)