1CK6

BINDING MODE OF SALICYLHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE

Summary for 1CK6

• Entry DOI: 10.2210/pdb1ck6/pdb
• Descriptor: PROTEIN (PEROXIDASE), 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, beta-D-mannopyranose, ... (7 entities in total)
• Functional Keywords: oxidoreductase, glycoprotein, peroxidase
• Biological source: 'Arthromyces ramosus'
• Total number of polymer chains: 1
• Total formula weight: 37177.13

Authors

Fukuyama, K.,Itakura, H. (deposition date: 1999-04-28, release date: 1999-12-29, Last modification date: 2024-10-30)

Primary citation

Tsukamoto, K.,Itakura, H.,Sato, K.,Fukuyama, K.,Miura, S.,Takahashi, S.,Ikezawa, H.,Hosoya, T.
Binding of salicylhydroxamic acid and several aromatic donor molecules to Arthromyces ramosus peroxidase, investigated by X-ray crystallography, optical difference spectroscopy, NMR relaxation, molecular dynamics, and kinetics.
Biochemistry, 38:12558-12568, 1999

PubMed Abstract: The X-ray crystal structure of the complex of salicylhydroxamic acid (SHA) with Arthromyces ramosus peroxidase (ARP) has been determined at 1.9 A resolution. The position of SHA in the active site of ARP is similar to that of the complex of benzhydroxamic acid (BHA) with ARP [Itakura, H., et al. (1997) FEBS Lett. 412, 107-110]. The aromatic ring of SHA binds to a hydrophobic region at the opening of the distal pocket, and the hydroxamic acid moiety forms hydrogen bonds with the His56, Arg52, and Pro154 residues but is not asscoiated with the heme iron. X-ray analyses of ARP-resorcinol and ARP-p-cresol complexes failed to identify the aromatic donor molecules, most likely due to the very low affinities of these aromatic donors for ARP. Therefore, we examined the locations of these and other aromatic donors on ARP by the molecular dynamics method and found that the benzene rings are trapped similarly by hydrophobic interactions with the Ala92, Pro156, Leu192, and Phe230 residues at the entrance of the heme pocket, but the dihedral angles between the benzene rings and the heme plane vary from donor to donor. The distances between the heme iron and protons of SHA and resorcinol are similar to those obtained by NMR relaxation. Although SHA and BHA are usually considered potent inhibitors for peroxidase, they were found to reduce compound I and compound II of ARP and horseradish peroxidase C in the same manner as p-cresol and resorcinol. The aforementioned spatial relationships of these aromatic donors to the heme iron in ARP are discussed with respect to the quantum chemical mechanism of electron transfer in peroxidase reactions.

PubMed: 10504224
DOI: 10.1021/bi982925l

Experimental method

X-RAY DIFFRACTION (1.9 Å)