PDBsum entry 1n4w

Oxidoreductase

PDB id: 1n4w

Contents

Protein chain

499 a.a. *

Ligands

FAD

GOL

Metals

_MN

Waters ×813

* Residue conservation analysis

PDB id:

1n4w

Name:

Oxidoreductase

Title:

Atomic resolution structure of cholesterol oxidase @ ph 7.3 (streptomyces sp. Sa-coo)

Structure:

Cholesterol oxidase. Chain: a. Synonym: chod. Engineered: yes. Other_details: fad cofactor non-covalently bound to the enzyme

Source:

Streptomyces sp.. Organism_taxid: 74576. Strain: sa-coo. Gene: choa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

0.92Å R-factor: 0.104 R-free: 0.122

Authors:

A.Vrielink,P.I.Lario

Key ref:

A.Y.Lyubimov et al. (2006). Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment. Nat Chem Biol, 2, 259-264. PubMed id: 16604066 DOI: 10.1038/nchembio784

Date:

01-Nov-02 Release date: 27-Apr-04

Protein chain

P12676  (CHOD_STRS0) -  Cholesterol oxidase from Streptomyces sp. (strain SA-COO)

Seq: 546 a.a.

Struc: 499 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.1.3.6 - cholesterol oxidase.
• Reaction: cholesterol + O2 = cholest-5-en-3-one + H2O2
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

• Enzyme class 3: E.C.5.3.3.1 - steroid Delta-isomerase.
• Reaction: a 3-oxo-Delta₅-steroid = a 3-oxo-Delta₄-steroid

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1038/nchembio784

Nat Chem Biol 2:259-264 (2006)

PubMed id: 16604066

Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment.

A.Y.Lyubimov, P.I.Lario, I.Moustafa, A.Vrielink.

ABSTRACT

Hydrogen atoms are a vital component of enzyme structure and function. In recent years, atomic resolution crystallography (>or=1.2 A) has been successfully used to investigate the role of the hydrogen atom in enzymatic catalysis. Here, atomic resolution crystallography was used to study the effect of pH on cholesterol oxidase from Streptomyces sp., a flavoenzyme oxidoreductase. Crystallographic observations of the anionic oxidized flavin cofactor at basic pH are consistent with the UV-visible absorption profile of the enzyme and readily explain the reversible pH-dependent loss of oxidation activity. Furthermore, a hydrogen atom, positioned at an unusually short distance from the main chain carbonyl oxygen of Met122 at high pH, was observed, suggesting a previously unknown mechanism of cofactor stabilization. This study shows how a redox active site responds to changes in the enzyme's environment and how these changes are able to influence the mechanism of enzymatic catalysis.

Selected figure(s)

Figure 4.
(a–e) Electron-density features around the imidazole ring of His447 at pH 4.5 (a), pH 5.2 (b), pH 5.8 (c), pH 7.3 (d) and pH 9.0 (e). (f) A view of the interactions between His447, Asn321 and Asn323 at pH 5.2. The 2F[o] – F[c] density (magenta) is contoured at 4.0 , and the sharpened F[o] – F[c] density (green) is contoured at 2.0 . The atoms are depicted by a ball-and-stick representation. The bifurcated hydrogen bonds formed by ND1 of His447 with the amide groups of Asn321 and Asn323 are drawn as blue dashed lines. The chemical structure of the histidine side chain with labeled atoms is included.

Figure 5.
(a) A model representing the microenvironment from pH 4.5 to 7.3, where FAD is in the neutral oxidized form and His447 is in the imidazole form protonated at NE2. (b) A model representing the microenvironment at pH 9.0, where the negative charge of the imidazolate form of His447 is stabilized by interaction with Asn321 and Asn323.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2006, 2, 259-264) copyright 2006.

Figures were selected by an automated process.