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PDBsum entry 1ff3

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1ff3
Jmol
Contents
Protein chains
211 a.a. *
194 a.a. *
Ligands
SO4 ×4
Waters ×530
* Residue conservation analysis
PDB id:
1ff3
Name: Oxidoreductase
Title: Structure of the peptide methionine sulfoxide reductase from escherichia coli
Structure: Peptide methionine sulfoxide reductase. Chain: a, b, c. Synonym: peptide met(o) reductase
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Hexamer (from PQS)
Resolution:
1.90Å     R-factor:   0.195     R-free:   0.218
Authors: F.Tete-Favier,D.Cobessi,S.Boschi-Muller,S.Azza,G.Branlant, A.Aubry
Key ref:
F.Tête-Favier et al. (2000). Crystal structure of the Escherichia coli peptide methionine sulphoxide reductase at 1.9 A resolution. Structure, 8, 1167-1178. PubMed id: 11080639 DOI: 10.1016/S0969-2126(00)00526-8
Date:
25-Jul-00     Release date:   06-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A744  (MSRA_ECOLI) -  Peptide methionine sulfoxide reductase MsrA
Seq:
Struc:
212 a.a.
211 a.a.*
Protein chains
Pfam   ArchSchema ?
P0A744  (MSRA_ECOLI) -  Peptide methionine sulfoxide reductase MsrA
Seq:
Struc:
212 a.a.
194 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.1.8.4.11  - Peptide-methionine (S)-S-oxide reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. Peptide-L-methionine + thioredoxin disulfide + H2O = peptide-L- methionine (S)-S-oxide + thioredoxin
2. L-methionine + thioredoxin disulfide + H2O = L-methionine (S)-S- oxide + thioredoxin
Peptide-L-methionine
+ thioredoxin disulfide
+ H(2)O
= peptide-L- methionine (S)-S-oxide
+ thioredoxin
L-methionine
+ thioredoxin disulfide
+ H(2)O
= L-methionine (S)-S- oxide
+ thioredoxin
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00526-8 Structure 8:1167-1178 (2000)
PubMed id: 11080639  
 
 
Crystal structure of the Escherichia coli peptide methionine sulphoxide reductase at 1.9 A resolution.
F.Tête-Favier, D.Cobessi, S.Boschi-Muller, S.Azza, G.Branlant, A.Aubry.
 
  ABSTRACT  
 
BACKGROUND: Peptide methionine sulphoxide reductases catalyze the reduction of oxidized methionine residues in proteins. They are implicated in the defense of organisms against oxidative stress and in the regulation of processes involving peptide methionine oxidation/reduction. These enzymes are found in numerous organisms, from bacteria to mammals and plants. Their primary structure shows no significant similarity to any other known protein. RESULTS: The X-ray structure of the peptide methionine sulphoxide reductase from Escherichia coli was determined at 3 A resolution by the multiple wavelength anomalous dispersion method for the selenomethionine-substituted enzyme, and it was refined to 1.9 A resolution for the native enzyme. The 23 kDa protein is folded into an alpha/beta roll and contains a large proportion of coils. Among the three cysteine residues involved in the catalytic mechanism, Cys-51 is positioned at the N terminus of an alpha helix, in a solvent-exposed area composed of highly conserved amino acids. The two others, Cys-198 and Cys-206, are located in the C-terminal coil. CONCLUSIONS: Sequence alignments show that the overall fold of the peptide methionine sulphoxide reductase from E. coli is likely to be conserved in many species. The characteristics observed in the Cys-51 environment are in agreement with the expected accessibility of the active site of an enzyme that reduces methionine sulphoxides in various proteins. Cys-51 could be activated by the influence of an alpha helix dipole. The involvement of the two other cysteine residues in the catalytic mechanism requires a movement of the C-terminal coil. Several conserved amino acids and water molecules are discussed as potential participants in the reaction.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Stereoview of the Active Site Region of MsrAThe figure was produced with MOLSCRIPT [48] and Raster3D [49]. Side chains of the amino acids around the catalytic residue Cys-51 are displayed as ball-and-stick representations

 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 1167-1178) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21210868 M.J.Kim, B.C.Lee, J.Jeong, K.J.Lee, K.Y.Hwang, V.N.Gladyshev, and H.Y.Kim (2011).
Tandem use of selenocysteine: adaptation of a selenoprotein glutaredoxin for reduction of selenoprotein methionine sulfoxide reductase.
  Mol Microbiol, 79, 1194-1203.  
19958171 N.Ugarte, I.Petropoulos, and B.Friguet (2010).
Oxidized mitochondrial protein degradation and repair in aging and oxidative stress.
  Antioxid Redox Signal, 13, 539-549.  
19400786 Y.K.Kim, Y.J.Shin, W.H.Lee, H.Y.Kim, and K.Y.Hwang (2009).
Structural and kinetic analysis of an MsrA-MsrB fusion protein from Streptococcus pneumoniae.
  Mol Microbiol, 72, 699-709.
PDB codes: 3e0m 3e0o
17500063 A.Gand, M.Antoine, S.Boschi-Muller, and G.Branlant (2007).
Characterization of the amino acids involved in substrate specificity of methionine sulfoxide reductase A.
  J Biol Chem, 282, 20484-20491.  
17493655 H.Zhu, P.Smith, L.K.Wang, and S.Shuman (2007).
Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase.
  Virology, 366, 126-136.
PDB code: 2ia5
17135266 N.Rouhier, B.Kauffmann, F.Tete-Favier, P.Palladino, P.Gans, G.Branlant, J.P.Jacquot, and S.Boschi-Muller (2007).
Functional and structural aspects of poplar cytosolic and plastidial type a methionine sulfoxide reductases.
  J Biol Chem, 282, 3367-3378.
PDB code: 2j89
17105189 H.Y.Kim, D.E.Fomenko, Y.E.Yoon, and V.N.Gladyshev (2006).
Catalytic advantages provided by selenocysteine in methionine-S-sulfoxide reductases.
  Biochemistry, 45, 13697-13704.  
17062561 M.Antoine, A.Gand, S.Boschi-Muller, and G.Branlant (2006).
Characterization of the amino acids from Neisseria meningitidis MsrA involved in the chemical catalysis of the methionine sulfoxide reduction step.
  J Biol Chem, 281, 39062-39070.  
16926157 N.Brot, J.F.Collet, L.C.Johnson, T.J.Jönsson, H.Weissbach, and W.T.Lowther (2006).
The thioredoxin domain of Neisseria gonorrhoeae PilB can use electrons from DsbD to reduce downstream methionine sulfoxide reductases.
  J Biol Chem, 281, 32668-32675.
PDB code: 2h30
15601707 B.Ezraty, J.Bos, F.Barras, and L.Aussel (2005).
Methionine sulfoxide reduction and assimilation in Escherichia coli: new role for the biotin sulfoxide reductase BisC.
  J Bacteriol, 187, 231-237.  
16262444 H.Y.Kim, and V.N.Gladyshev (2005).
Different catalytic mechanisms in mammalian selenocysteine- and cysteine-containing methionine-R-sulfoxide reductases.
  PLoS Biol, 3, e375.  
15668226 J.Wu, F.Neiers, S.Boschi-Muller, and G.Branlant (2005).
The N-terminal domain of PILB from Neisseria meningitidis is a disulfide reductase that can recycle methionine sulfoxide reductases.
  J Biol Chem, 280, 12344-12350.  
15590653 K.F.Fulton, A.M.Buckle, L.D.Cabrita, J.A.Irving, R.E.Butcher, I.Smith, S.Reeve, A.M.Lesk, S.P.Bottomley, J.Rossjohn, and J.C.Whisstock (2005).
The high resolution crystal structure of a native thermostable serpin reveals the complex mechanism underpinning the stressed to relaxed transition.
  J Biol Chem, 280, 8435-8442.
PDB code: 1sng
16077131 P.Vattanaviboon, C.Seeanukun, W.Whangsuk, S.Utamapongchai, and S.Mongkolsuk (2005).
Important role for methionine sulfoxide reductase in the oxidative stress response of Xanthomonas campestris pv. phaseoli.
  J Bacteriol, 187, 5831-5836.  
15558583 Y.Qi, and N.V.Grishin (2005).
Structural classification of thioredoxin-like fold proteins.
  Proteins, 58, 376-388.  
15280355 F.Neiers, A.Kriznik, S.Boschi-Muller, and G.Branlant (2004).
Evidence for a new sub-class of methionine sulfoxide reductases B with an alternative thioredoxin recognition signature.
  J Biol Chem, 279, 42462-42468.  
15756465 N.Coudevylle, A.Thureau, S.Azza, S.Boshi-Muller, G.Branlant, and M.T.Cung (2004).
(1)H, (13)C and (15)N resonance assignment of the reduced form of methionine sulfoxide reductase A from Escherichia coli.
  J Biomol NMR, 30, 363-364.  
12837786 A.B.Taylor, D.M.Benglis, S.Dhandayuthapani, and P.J.Hart (2003).
Structure of Mycobacterium tuberculosis methionine sulfoxide reductase A in complex with protein-bound methionine.
  J Bacteriol, 185, 4119-4126.
PDB code: 1nwa
14675542 C.V.Smith, and J.C.Sacchettini (2003).
Mycobacterium tuberculosis: a model system for structural genomics.
  Curr Opin Struct Biol, 13, 658-664.  
12954610 M.Antoine, S.Boschi-Muller, and G.Branlant (2003).
Kinetic characterization of the chemical steps involved in the catalytic mechanism of methionine sulfoxide reductase A from Neisseria meningitidis.
  J Biol Chem, 278, 45352-45357.  
12777806 P.Retailleau, and T.Prangé (2003).
Phasing power at the K absorption edge of organic arsenic.
  Acta Crystallogr D Biol Crystallogr, 59, 887-896.
PDB code: 1n4f
11812798 A.Olry, S.Boschi-Muller, M.Marraud, S.Sanglier-Cianferani, A.Van Dorsselear, and G.Branlant (2002).
Characterization of the methionine sulfoxide reductase activities of PILB, a probable virulence factor from Neisseria meningitidis.
  J Biol Chem, 277, 12016-12022.  
12198304 B.Kauffmann, F.Favier, A.Olry, S.Boschi-Muller, P.Carpentier, G.Branlant, and A.Aubry (2002).
Crystallization and preliminary X-ray diffraction studies of the peptide methionine sulfoxide reductase B domain of Neisseria meningitidis PILB.
  Acta Crystallogr D Biol Crystallogr, 58, 1467-1469.  
11929995 G.V.Kryukov, R.A.Kumar, A.Koc, Z.Sun, and V.N.Gladyshev (2002).
Selenoprotein R is a zinc-containing stereo-specific methionine sulfoxide reductase.
  Proc Natl Acad Sci U S A, 99, 4245-4250.  
12145281 R.A.Kumar, A.Koc, R.L.Cerny, and V.N.Gladyshev (2002).
Reaction mechanism, evolutionary analysis, and role of zinc in Drosophila methionine-R-sulfoxide reductase.
  J Biol Chem, 277, 37527-37535.  
11938352 W.T.Lowther, H.Weissbach, F.Etienne, N.Brot, and B.W.Matthews (2002).
The mirrored methionine sulfoxide reductases of Neisseria gonorrhoeae pilB.
  Nat Struct Biol, 9, 348-352.
PDB code: 1l1d
11604533 S.Boschi-Muller, S.Azza, and G.Branlant (2001).
E. coli methionine sulfoxide reductase with a truncated N terminus or C terminus, or both, retains the ability to reduce methionine sulfoxide.
  Protein Sci, 10, 2272-2279.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.