2E3B

Crystal structure of the HA-bound form of Arthromyces ramosus peroxidase at 1.3 Angstroms resolution

Summary for 2E3B

• Entry DOI: 10.2210/pdb2e3b/pdb
• Related: 1ARP 2E39 2E3A
• Descriptor: Peroxidase, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose, ... (7 entities in total)
• Functional Keywords: heme protein, coordination geometry of heme iron, arp, peroxidase, oxidoreductase
• Biological source: 'Arthromyces ramosus'
• Cellular location: Secreted: P28313
• Total number of polymer chains: 1
• Total formula weight: 37057.03

Authors

Fukuyama, K.,Okada, T. (deposition date: 2006-11-22, release date: 2007-03-20, Last modification date: 2024-10-16)

Primary citation

Fukuyama, K.,Okada, T.
Structures of cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosusperoxidase at 100 K refined to 1.3 A resolution: coordination geometries of the ligands to the haem iron
ACTA CRYSTALLOGR.,SECT.D, 63:472-477, 2007

PubMed Abstract: 1.3 A resolution crystal structures of the cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosus peroxidase (ARP), a class II peroxidase belonging to the plant peroxidase superfamily, have been determined. Anisotropic temperature factors were introduced for all non-H atoms of these complexes using SHELX-97 and stereochemical constraints were applied to the protein, protoporphyrin and sugar moieties, but not to the coordination geometries to the haem iron. These refinements identified multiple conformations for several side chains and revised the side-chain conformations of several residues. Little difference was observed in the structures of the polypeptides, haem and sugar moieties and in the coordinations to two calcium ions in these complexes. Characteristic coordination geometries of each ligand to the haem iron were observed. CN(-) binds to the haem iron in a tilt mode (Fe...C-N = 170 degrees ), whereas NO and hydroxylamine bind in bent modes (Fe...N-O = 125 degrees and Fe...NH(2)-OH = 111 degrees ). CN(-) is directed toward the distal histidine (His56) and forms a hydrogen bond with the N(epsilon) atom, whereas NO and hydroxylamine are directed away from His56. The Fe atoms of ARP-CN and ARP-NO, in which the haem irons are both in low-spin states, are approximately in the pyrrole N plane, whereas the iron in native ARP, which is in a five-coordinated high-spin state, deviates markedly from the plane.

PubMed: 17372351
DOI: 10.1107/S0907444907003812

Experimental method

X-RAY DIFFRACTION (1.3 Å)