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(-) Description

Title :  STRUCTURE OF THE PEPTIDE METHIONINE SULFOXIDE REDUCTASE FROM ESCHERICHIA COLI
 
Authors :  F. Tete-Favier, D. Cobessi, S. Boschi-Muller, S. Azza, G. Branlant, A. Aubry
Date :  25 Jul 00  (Deposition) - 06 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A (2x),B (2x),C (2x)
Biol. Unit 5:  A,B  (2x)
Biol. Unit 6:  A (1x),C (1x)
Keywords :  Peptide Methionine Sulfoxide Reductase, Alpha Beta Roll, Pmsr, Msra, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Tete-Favier, D. Cobessi, S. Boschi-Muller, S. Azza, G. Branlant, A. Aubry
Crystal Structure Of The Escherichia Coli Peptide Methionine Sulphoxide Reductase At 1. 9 A Resolution.
Structure Fold. Des. V. 8 1167 2000
PubMed-ID: 11080639  |  Reference-DOI: 10.1016/S0969-2126(00)00526-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE METHIONINE SULFOXIDE REDUCTASE
    Chains: A, B, C
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PEPTIDE MET(O) REDUCTASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (2x): A (2x)B (2x)C (2x)
Biological Unit 5 (2x): AB 
Biological Unit 6 (1x): A (1x) C (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CAS3Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CAS-1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (2, 12)
No.NameCountTypeFull Name
1CAS4Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2SO48Ligand/IonSULFATE ION
Biological Unit 6 (2, 4)
No.NameCountTypeFull Name
1CAS1Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2SO43Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:81 , ARG A:83 , HOH A:602 , HOH A:639BINDING SITE FOR RESIDUE SO4 A 533
2AC2SOFTWARESER A:1 , LYS A:5 , LYS A:6 , HIS A:7 , HIS B:7BINDING SITE FOR RESIDUE SO4 A 534
3AC3SOFTWAREARG A:18 , ASN A:19 , THR A:20 , HOH A:759BINDING SITE FOR RESIDUE SO4 A 535
4AC4SOFTWAREARG B:18 , ASN B:19 , THR B:20BINDING SITE FOR RESIDUE SO4 B 536

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:206 -B:86

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FF3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FF3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FF3)

(-) Exons   (0, 0)

(no "Exon" information available for 1FF3)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:211
 aligned with MSRA_ECOLI | P0A744 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
           MSRA_ECOLI     2 SLFDKKHLVSPADALPGRNTPMPVATLHAVNGHSMTNVPDGMEIAIFAMGCFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVCSGDTGHAEAVRIVYDPSVISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQDAAARASLERFQAAMLAADDDRHITTEIANATPFYYAEDDHQQYLHKNPYGYCGIGGIGVCLPPEA 212
               SCOP domains d1ff3a_ A: Peptide methionine sulfoxide reductase                                                                                                                                                                   SCOP domains
               CATH domains 1ff3A00 A:1-211 Peptide Methionine Sulfoxide Reductase; Chain A                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh............................eeeeee...hhhhhhhhhh...eeeeeeeee.......hhhhhhhh....eeeeeeee.....hhhhhhhhhhhh.......ee..ee.hhhh.ee...hhhhhhhhhhhhhhhhhhhhhh........ee.....eee.hhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ff3 A   1 SLFDKKHLVSPADALPGRNTPMPVATLHAVNGHSMTNVPDGMEIAIFAMGcFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVCSGDTGHAEAVRIVYDPSVISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQDAAARASLERFQAAMLAADDDRHITTEIANATPFYYAEDDHQQYLHKNPYGYCGIGGIGVCLPPEA 211
                                    10        20        30        40        50|       60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
                                                                             51-CAS                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with MSRA_ECOLI | P0A744 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:194
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191    
           MSRA_ECOLI     2 SLFDKKHLVSPADALPGRNTPMPVATLHAVNGHSMTNVPDGMEIAIFAMGCFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVCSGDTGHAEAVRIVYDPSVISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQDAAARASLERFQAAMLAADDDRHITTEIANATPFYYAEDDHQQYLHKNP 195
               SCOP domains d1ff3b_ B: Peptide methionine sulfoxide reductase                                                                                                                                                  SCOP domains
               CATH domains 1ff3B00 B:1-194 Peptide Methionine Sulfoxide Reductase; Chain A                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..................................eeeeeee..hhhhhhhhhh...eeeeeeeee.......hhhhhhhh....eeeeeeee.....hhhhhhhhhhhh.......ee..ee.hhh.eee...hhhhhhhhhhhhhhhhhhhhhh........ee......ee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ff3 B   1 SLFDKKHLVSPADALPGRNTPMPVATLHAVNGHSMTNVPDGMEIAIFAMGcFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVCSGDTGHAEAVRIVYDPSVISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQDAAARASLERFQAAMLAADDDRHITTEIANATPFYYAEDDHQQYLHKNP 194
                                    10        20        30        40        50|       60        70        80        90       100       110       120       130       140       150       160       170       180       190    
                                                                             51-CAS                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:185
 aligned with MSRA_ECOLI | P0A744 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:185
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     
           MSRA_ECOLI     9 LVSPADALPGRNTPMPVATLHAVNGHSMTNVPDGMEIAIFAMGCFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVCSGDTGHAEAVRIVYDPSVISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQDAAARASLERFQAAMLAADDDRHITTEIANATPFYYAEDDHQQYLHK 193
               SCOP domains d1ff3c_ C: Peptide methionine sulfoxide reductase                                                                                                                                         SCOP domains
               CATH domains 1ff3C00 C:8-192 Peptide Methionine Sulfoxide Reductase; Chain A                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................eeeeeee..hhhhhhhhhh...eeeeeeeee.......hhhhhhh.....eeeeeeee.....hhhhhhhhhhhh.......ee..ee.hhh.eee...hhhhhhhhhhhhhhhhhhhhhh........ee......ee.hhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ff3 C   8 LVSPADALPGRNTPMPVATLHAVNGHSMTNVPDGMEIAIFAMGcFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVCSGDTGHAEAVRIVYDPSVISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQDAAARASLERFQAAMLAADDDRHITTEIANATPFYYAEDDHQQYLHK 192
                                    17        27        37        47   |    57        67        77        87        97       107       117       127       137       147       157       167       177       187     
                                                                      51-CAS
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FF3)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (MSRA_ECOLI | P0A744)
molecular function
    GO:0036456    L-methionine-(S)-S-oxide reductase activity    Catalysis of the reaction: L-methionine (S)-S-oxide + thioredoxin -> L-methionine + thioredoxin disulfide + H2O.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    GO:0008113    peptide-methionine (S)-S-oxide reductase activity    Catalysis of the reactions: peptide-L-methionine + thioredoxin disulfide + H2O = peptide-L-methionine (S)-S-oxide + thioredoxin, and L-methionine + thioredoxin disulfide + H2O = L-methionine (S)-S-oxide + thioredoxin. Can act on oxidized methionine in peptide linkage with specificity for the S enantiomer. Thioredoxin disulfide is the oxidized form of thioredoxin.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0030091    protein repair    The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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        MSRA_ECOLI | P0A744: 2gt3 2iem

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