PDBsum entry 1k3i

Oxidoreductase

PDB id: 1k3i

Contents

Protein chain

651 a.a. *

Ligands

GLC

ACT ×2

Metals

_CA ×2

Waters ×684

* Residue conservation analysis

PDB id:

1k3i

Name:

Oxidoreductase

Title:

Crystal structure of the precursor of galactose oxidase

Structure:

Galactose oxidase precursor. Chain: a. Engineered: yes

Source:

Fusarium sp.. Organism_taxid: 29916. Expressed in: emericella nidulans. Expression_system_taxid: 162425.

Resolution:

1.40Å R-factor: 0.176 R-free: 0.193

Authors:

S.J.Firbank,M.S.Rogers,C.M.Wilmot,D.M.Dooley,M.A.Halcrow,P.F.Knowles, M.J.Mcpherson,S.E.V.Phillips

Key ref:

S.J.Firbank et al. (2001). Crystal structure of the precursor of galactose oxidase: an unusual self-processing enzyme. Proc Natl Acad Sci U S A, 98, 12932-12937. PubMed id: 11698678 DOI: 10.1073/pnas.231463798

Date:

03-Oct-01 Release date: 07-Nov-01

Protein chain

P0CS93  (GAOA_GIBZA) -  Galactose oxidase from Gibberella zeae

Seq: 680 a.a.

Struc: 651 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.1.3.9 - galactose oxidase.
• Reaction: D-galactose + O2 = D-galacto-hexodialdose + H2O2

D-galactose (Bound ligand (Het Group name = GLC) matches with 75.00% similarity) + O2 = D-galacto-hexodialdose + H2O2

• Cofactor: Cu cation

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

reference

DOI no: 10.1073/pnas.231463798

Proc Natl Acad Sci U S A 98:12932-12937 (2001)

PubMed id: 11698678

Crystal structure of the precursor of galactose oxidase: an unusual self-processing enzyme.

S.J.Firbank, M.S.Rogers, C.M.Wilmot, D.M.Dooley, M.A.Halcrow, P.F.Knowles, M.J.McPherson, S.E.Phillips.

ABSTRACT

Galactose oxidase (EC ) is a monomeric enzyme that contains a single copper ion and catalyses the stereospecific oxidation of primary alcohols to their corresponding aldehydes. The protein contains an unusual covalent thioether bond between a tyrosine, which acts as a radical center during the two-electron reaction, and a cysteine. The enzyme is produced in a precursor form lacking the thioether bond and also possessing an additional 17-aa pro-sequence at the N terminus. Previous work has shown that the aerobic addition of Cu(2+) to the precursor is sufficient to generate fully processed mature enzyme. The structure of the precursor protein has been determined to 1.4 A, revealing the location of the pro-sequence and identifying structural differences between the precursor and the mature protein. Structural alignment of the precursor and mature forms of galactose oxidase shows that five regions of main chain and some key residues of the active site differ significantly between the two forms. The precursor structure provides a starting point for modeling the chemistry of thioether bond formation and pro-sequence cleavage.

Selected figure(s)

Figure 1.
Fig. 1. Structure of the mature form of galactose oxidase (Upper Left) and the precursor form (Upper Right). Domain I is red, domain II is blue, and domain III is purple. In the precursor form the N-terminal pro-sequence is green, and regions that differ from the mature structure by more than 2 Å are yellow. The sequence of galactose oxidase (14) is shown (Lower) and colored as above. The pro-sequence residues are numbered 17 to 1. All figures were produced by using SPOCK (45).

Figure 3.
Fig. 3. Active site residues in precursor galactose oxidase (Left) and in the mature protein (Center) showing the copper ligands (Tyr-272, Tyr-495, His-496, and His-581), Cys-228 that forms the thioether bond to Tyr-272, the tryptophan that stacks over it (Trp-290), and Phe-227. The S of Cys-228 in the precursor is situated directly above C [2] of Tyr-272. In the precursor the sulfur of the cysteine appears to have been oxidized to a sulfenic group. (Right) Final 2F[o] F[c] electron density map for Cys-228 and Tyr-272.

Figures were selected by the author.