PDBsum entry 2e39

Oxidoreductase

PDB id: 2e39

Contents

Protein chain

336 a.a. *

Ligands

NAG-NAG

MAN

CYN-HEM

Metals

_CA ×2

Waters ×387

* Residue conservation analysis

PDB id:

2e39

Name:

Oxidoreductase

Title:

Crystal structure of the cn-bound form of arthromyces ramosus peroxidase at 1.3 angstroms resolution

Structure:

Peroxidase. Chain: a. Ec: 1.11.1.7

Source:

'Arthromyces ramosus'. Organism_taxid: 5451

Resolution:

1.30Å R-factor: 0.153 R-free: 0.203

Authors:

K.Fukuyama,T.Okada

Key ref:

K.Fukuyama and T.Okada (2007). 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 D Biol Crystallogr, 63, 472-477. PubMed id: 17372351 DOI: 10.1107/S0907444907003812

Date:

22-Nov-06 Release date: 20-Mar-07

Protein chain

P28313  (PER_ARTRA) -  Peroxidase from Arthromyces ramosus

Seq: 364 a.a.

Struc: 336 a.a.

Enzyme reactions

• Enzyme class: E.C.1.11.1.7 - peroxidase.
• Reaction: 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O
• Cofactor: Heme

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1107/S0907444907003812

Acta Crystallogr D Biol Crystallogr 63:472-477 (2007)

PubMed id: 17372351

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.

K.Fukuyama, T.Okada.

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.

Selected figure(s)

Figure 1.
Figure 1 Schematic representation of ARP. The haem group is shown in red and calcium ions in orange. The carbohydrates are shown as stick models, in which C, N and O atoms are in yellow, blue and red, respectively. This figure was prepared with the program PyMOL (DeLano, 2002[DeLano, W. L. (2002). The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA.]).

Figure 4.
Figure 4 Conformations of sugar moieties. (a) Two N-acetylglucosamine residues bound to Asn143 and (b) mannose residue bound to Ser339. The stick models are superimposed on the (2F[o] - F[c]) map contoured at the 1.5 level.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 472-477) copyright 2007.

Figures were selected by an automated process.