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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL METHIONINE SULFOXIDE REDUCTASE DOMAIN (MSRB) OF N. GONORRHOEAE PILB
 
Authors :  W. T. Lowther, H. Weissbach, F. Etienne, N. Brot, B. W. Matthews
Date :  15 Feb 02  (Deposition) - 01 May 02  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  B  (2x)
Keywords :  Cacodylate Complex, Cys-Arg-Asp Catalytic Triad, Met-R(O) Reductase, Oxidoreductase, Msrb (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. T. Lowther, H. Weissbach, F. Etienne, N. Brot, B. W. Matthews
The Mirrored Methionine Sulfoxide Reductases Of Neisseria Gonorrhoeae Pilb.
Nat. Struct. Biol. V. 9 348 2002
PubMed-ID: 11938352

(-) Compounds

Molecule 1 - PEPTIDE METHIONINE SULFOXIDE REDUCTASE
    ChainsA, B
    EC Number1.8.4.13, 1.8.4.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentMSRB DOMAIN, C-TERMINAL DOMAIN
    GenePILB
    Organism ScientificNEISSERIA GONORRHOEAE
    Organism Taxid485

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (2x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CAC3Ligand/IonCACODYLATE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1CAC4Ligand/IonCACODYLATE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1 , HOH A:110 , HOH A:112 , THR A:403 , TRP A:442 , GLY A:479 , HIS A:480 , CYS A:495BINDING SITE FOR RESIDUE CAC A 601
2AC2SOFTWAREHOH A:105 , GLU A:393 , ALA A:402 , THR A:403 , TYR A:405 , LYS B:387BINDING SITE FOR RESIDUE CAC B 602
3AC3SOFTWARELYS A:387 , HOH B:34 , HOH B:43 , GLU B:393 , ALA B:402 , THR B:403BINDING SITE FOR RESIDUE CAC B 603

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:440 -A:495
2B:440 -B:495

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L1D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L1D)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MSRBPS51790 Methionine-R-sulfoxide reductase (MsrB) domain profile.MSRAB_NEIGO383-506
 
  2A:383-506
B:383-506
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MSRBPS51790 Methionine-R-sulfoxide reductase (MsrB) domain profile.MSRAB_NEIGO383-506
 
  1A:383-506
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MSRBPS51790 Methionine-R-sulfoxide reductase (MsrB) domain profile.MSRAB_NEIGO383-506
 
  1-
B:383-506
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MSRBPS51790 Methionine-R-sulfoxide reductase (MsrB) domain profile.MSRAB_NEIGO383-506
 
  2-
B:383-506

(-) Exons   (0, 0)

(no "Exon" information available for 1L1D)

(-) 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:144
 aligned with MSRAB_NEIGO | P14930 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:144
                                   387       397       407       417       427       437       447       457       467       477       487       497       507       517    
          MSRAB_NEIGO   378 YKKPSDAELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKSVTEHDDFSFNMRRTEVRSRAADSHLGHVFPDGPRDKGGLRYCINGASLKFIPLEQMDAAGYGALKGEV 521
               SCOP domains d1l1da_ A: C-terminal MsrB domain of peptide methionine sulfoxide reductase PilB                                                                 SCOP domains
               CATH domains 1l1dA00 A:378-521 Peptide methionine sulfoxide reductase.                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh...hhhhhhhhhhh.......hhhhhh...eeeee.....eeee...ee.......ee........eeeeee......eeeeee.....eeeeee...hhhhh..eeee....eeeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----MSRB  PDB: A:383-506 UniProt: 383-506                                                                                       --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l1d A 378 YKKPSDAELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKSVTEHDDFSFNmRRTEVRSRAADSHLGHVFPDGPRDKGGLRYCINGASLKFIPLEQmDAAGYGALKGEV 521
                                   387       397       407       417       427       437       447       457      |467       477       487       497       507 |     517    
                                                                                                                464-MSE                                      509-MSE        

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with MSRAB_NEIGO | P14930 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:147
                                   384       394       404       414       424       434       444       454       464       474       484       494       504       514       
          MSRAB_NEIGO   375 AATYKKPSDAELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKSVTEHDDFSFNMRRTEVRSRAADSHLGHVFPDGPRDKGGLRYCINGASLKFIPLEQMDAAGYGALKGEV 521
               SCOP domains d1l1db_ B: C-terminal MsrB domain of peptide methionine sulfoxide reductase PilB                                                                    SCOP domains
               CATH domains 1l1dB00 B:375-521 Peptide methionine sulfoxide reductase.                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhh.......hhhhhh...eeeee.....eeee...ee.......ee........eeeeee......eeeeee.....eeeeee..........eeee....eeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------MSRB  PDB: B:383-506 UniProt: 383-506                                                                                       --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l1d B 375 AATYKKPSDAELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKSVTEHDDFSFNmRRTEVRSRAADSHLGHVFPDGPRDKGGLRYCINGASLKFIPLEQmDAAGYGALKGEV 521
                                   384       394       404       414       424       434       444       454       464       474       484       494       504    |  514       
                                                                                                                   464-MSE                                      509-MSE        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1L1D)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MSRAB_NEIGO | P14930)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0033743    peptide-methionine (R)-S-oxide reductase activity    Catalysis of the reaction: peptide-L-methionine + H(2)O + thioredoxin disulfide = peptide-L-methionine (R)-S-oxide + thioredoxin. Can act on oxidized methionine in peptide linkage with specificity for the R enantiomer. Thioredoxin disulfide is the oxidized form of thioredoxin.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.

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        MSRAB_NEIGO | P149302h30

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