Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN METHIONINE-R-SULFOXIDE REDUCTASE B1 (MSRB1)
 
Authors :  A. Chaikuad, N. Shafqat, W. W. Yue, P. Savitsky, T. Krojer, E. Ugochukwu, J. R. C. Muniz, A. C. W. Pike, F. Von Delft, C. H Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, U. Oppermann, Structural Genomics Consortium (Sgc)
Date :  24 Mar 10  (Deposition) - 07 Apr 10  (Release) - 07 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Structural Genomics Consortium, Sgc, Cytoplasm, Metal-Binding, Nucleus, Selenocysteine, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Chaikuad, N. Shafqat, W. W. Yue, P. Savitsky, T. Krojer, E. Ugochukwu, J. R. C. Muniz, A. C. W. Pike, F. Von Delft, C. H Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, U. Oppermann, Structural Genomics Consortium (Sgc)
Crystal Structure Of Human Methionine-R-Sulfoxide Reductase B1 (Msrb1)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHIONINE-R-SULFOXIDE REDUCTASE B1
    ChainsA
    EC Number1.8.4.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3-PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentMETHIONINE-R-SULFOXIDE REDUCTASE B1
    GeneHSPC270, MSRB1, SEPX1, SEPX1 (MSRB1)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMSRB1, SELENOPROTEIN X, SELX

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2MLI2Ligand/IonMALONATE ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:23 , CYS A:26 , CYS A:71 , CYS A:74BINDING SITE FOR RESIDUE FE A 1
2AC2SOFTWAREHOH A:8 , GLU A:60 , ARG A:63 , ALA A:66 , HOH A:159 , HOH A:187BINDING SITE FOR RESIDUE NA A 2
3AC3SOFTWARESER A:-1 , GLU A:48 , THR A:49 , HOH A:205 , HOH A:225 , HOH A:244BINDING SITE FOR RESIDUE NA A 3
4AC4SOFTWARESER A:41 , TRP A:43 , ARG A:63 , PHE A:82 , ARG A:93 , SER A:95 , LYS A:106 , GLY A:107 , LYS A:108 , GLU A:109 , HOH A:115 , HOH A:127 , HOH A:248BINDING SITE FOR RESIDUE MLI A 4
5AC5SOFTWAREVAL A:20 , SER A:32 , ARG A:34 , TRP A:43 , PHE A:97 , SER A:98 , HOH A:156 , HOH A:167 , HOH A:184BINDING SITE FOR RESIDUE MLI A 5

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MAO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MAO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MAO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MAO)

(-) Exons   (0, 0)

(no "Exon" information available for 3MAO)

(-) Sequences/Alignments

Asymmetric/Biological 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:105
 aligned with MSRB1_HUMAN | Q9NZV6 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:105
                                    17        27        37        47        57        67        77        87        97       107     
          MSRB1_HUMAN     8 GGEVFQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHADSVAKRPEHNRSEALKVSCGKCGNGLGHEFLNDGPKPGQSRFUIFSSSLKFVPKGKETSA 112
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --SelR-3maoA01 A:10-106                                                                            ------ Pfam domains
         Sec.struct. author ...........eeeee.....eeee...ee.......ee........eeeee......eeeeee.....eeeeee..........eeee....eeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3mao A  -1 SMEVFQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHADSVAKRPEHNRSEALKVSCGKCGNGLGHEFLNDGPKPGQSRFSIFSSSLKFVPKGKETSA 112
                             ||     17        27        37        47        57        67        77        87        97       107     
                             0|                                                                                                      
                             10                                                                                                      

   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  (0, 0)

(no "SCOP Domain" information available for 3MAO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MAO)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MSRB1_HUMAN | Q9NZV6)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0070191    methionine-R-sulfoxide reductase activity    Catalysis of the reaction: L-methionine R-oxide + thioredoxin = L-methionine + thioredoxin disulfide; can act on free oxidized methionine with specificity for the R enantiomer; does not act on oxidized methionine in peptide linkage. Thioredoxin disulfide is the oxidized form of thioredoxin.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030041    actin filament polymerization    Assembly of actin filaments by the addition of actin monomers to a filament.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mao)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3mao
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MSRB1_HUMAN | Q9NZV6
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.8.4.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MSRB1_HUMAN | Q9NZV6
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3MAO)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3MAO)