PDBsum entry 1l1d

Oxidoreductase

PDB id: 1l1d

Contents

Protein chains

144 a.a. *

Ligands

CAC ×3

Waters ×124

* Residue conservation analysis

PDB id:

1l1d

Name:

Oxidoreductase

Title:

Crystal structure of thE C-terminal methionine sulfoxide reductase domain (msrb) of n. Gonorrhoeae pilb

Structure:

Peptide methionine sulfoxide reductase. Chain: a, b. Fragment: msrb domain, c-terminal domain. Engineered: yes

Source:

Neisseria gonorrhoeae. Organism_taxid: 485. Gene: pilb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.85Å R-factor: 0.207 R-free: 0.237

Authors:

W.T.Lowther,H.Weissbach,F.Etienne,N.Brot,B.W.Matthews

Key ref:

W.T.Lowther et al. (2002). The mirrored methionine sulfoxide reductases of Neisseria gonorrhoeae pilB. Nat Struct Biol, 9, 348-352. PubMed id: 11938352 DOI: 10.1038/nsb783

Date:

15-Feb-02 Release date: 01-May-02

Protein chains

P14930  (MSRAB_NEIGO) -  Peptide methionine sulfoxide reductase MsrA/MsrB from Neisseria gonorrhoeae

Seq: 522 a.a.

Struc: 144 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.8.4.11 - peptide-methionine (S)-S-oxide reductase.
• Reaction:
  1. L-methionyl-[protein] + [thioredoxin]-disulfide + H2O = L-methionyl- (S)-S-oxide-[protein] + [thioredoxin]-dithiol
  2. [thioredoxin]-disulfide + L-methionine + H2O = L-methionine (S)-S- oxide + [thioredoxin]-dithiol
• Enzyme class 3: E.C.1.8.4.12 - peptide-methionine (R)-S-oxide reductase.
• Reaction: L-methionyl-[protein] + [thioredoxin]-disulfide + H2O = L-methionyl-(R)- S-oxide-[protein] + [thioredoxin]-dithiol
• Cofactor: Se(2+); Zn(2+)

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/nsb783

Nat Struct Biol 9:348-352 (2002)

PubMed id: 11938352

The mirrored methionine sulfoxide reductases of Neisseria gonorrhoeae pilB.

W.T.Lowther, H.Weissbach, F.Etienne, N.Brot, B.W.Matthews.

ABSTRACT

Methionine sulfoxide reductases (Msr) protect against oxidative damage that can contribute to cell death. The tandem Msr domains (MsrA and MsrB) of the pilB protein from Neisseria gonorrhoeae each reduce different epimeric forms of methionine sulfoxide. The overall fold of the MsrB domain revealed by the 1.85 A crystal structure shows no resemblance to the previously determined MsrA structures from other organisms. Despite the lack of homology, the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulfenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulfide exchange steps involving another active site Cys residue and thioredoxin. These observations have broad implications for modular catalysis, antibiotic drug design and continuing longevity studies in mammals.

Selected figure(s)

Figure 3.
Figure 3. Mirror-like relationship between the active sites of MsrB and MsrA domains. a, Model for the interactions of Met-R(O) (orange carbon atoms) with the active site of the pilB MsrB domain (this work). b, Model for the interaction of Met-S(O) with the active site of bovine MsrA^16. In each case, only small adjustments to the rotamer angle of the presumed nucleophilic Cys residue, Cys 495 or Cys 72, were required to establish a feasible interaction ( 2.1 Å) with the sulfur atom of the sulfoxide moiety (dashed yellow lines). The substrates were also docked in a manner to place the oxygen and sulfur atoms at the axial positions of the putative trigonal-bipyramidal intermediate of the reaction (Fig. 4). The MsrA domain of pilB presumably shows interactions similar to those here because the active site residues are conserved and the overall sequence identity is 40% (ref. 15).

Figure 4.
Figure 4. Proposed reaction mechanism for MsrB catalysis. The active site residues and the solvent molecule, W 1, are indicated in bold. The nucleophilic attack by Cys 495 (I) results in a trigonal-bipyramidal intermediate (II). Collapse of the intermediate leads to the formation of a sulfenic acid derivative of Cys 495 and the release of methionine (III). The analogous derivative within the MsrB homolog SelX probably contains a selenenic acid modification (Fig. 2a). A series of thiol-disulfide exchange reactions (III and IV) and the action of reducing thiols, either dithiothreitol (DTT) in vitro or the thioredoxin-thioredoxin reductase system (TR/TRR) with its associated cofactor NADPH in vivo, return the active site to the fully reduced state. Whether the addition of the proton to the oxygen atom of the sulfoxide moiety occurs between steps I and II or steps II and III, as shown, remains to be determined.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 348-352) copyright 2002.

Figures were selected by an automated process.