2VLY image
Entry Detail
PDB ID:
2VLY
Title:
Crystal structure of myoglobin compound III (radiation-induced)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2008-01-20
Release Date:
2008-01-29
Method Details:
Experimental Method:
Resolution:
1.60 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:MYOGLOBIN
Chain IDs:A
Chain Length:153
Number of Molecules:1
Biological Source:EQUUS CABALLUS
Primary Citation
The Crystal Structure of Peroxymyoglobin Generated Through Cryoradiolytic Reduction of Myoglobin Compound III During Data Collection.
Biochem.J. 412 257 ? (2008)
PMID: 18215120 DOI: 10.1042/BJ20070921

Abstact

Myoglobin has the ability to react with hydrogen peroxide, generating high-valent complexes similar to peroxidases (compounds I and II), and in the presence of excess hydrogen peroxide a third intermediate, compound III, with an oxymyoglobin-type structure is generated from compound II. The compound III is, however, easily one-electron reduced to peroxymyoglobin by synchrotron radiation during crystallographic data collection. We have generated and solved the 1.30 A (1 A=0.1 nm) resolution crystal structure of the peroxymyoglobin intermediate, which is isoelectric to compound 0 and has a Fe-O distance of 1.8 A and O-O bond of 1.3 A in accordance with a Fe(II)-O-O- (or Fe(III)-O-O2-) structure. The generation of the peroxy intermediate through reduction of compound III by X-rays shows the importance of using single-crystal microspectrophotometry when doing crystallography on metalloproteins. After having collected crystallographic data on a peroxy-generated myoglobin crystal, we were able (by a short annealing) to break the O-O bond leading to formation of compound II. These results indicate that the cryoradiolytic-generated peroxymyoglobin is biologically relevant through its conversion into compound II upon heating. Additionally, we have observed that the Xe1 site is occupied by a water molecule, which might be the leaving group in the compound II to compound III reaction.

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