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 THE PUTATIVE VITAMIN-B12 INDEPENDENT METHIONINE SYNTHASE FROM LISTERIA MONOCYTOGENES, NORTHEAST STRUCTURAL GENOMICS TARGET LMR13
 
Authors :  F. Forouhar, Y. Chen, J. Benach, R. Xiao, T. B. Acton, G. T. Montelione, J L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  31 Jan 05  (Deposition) - 08 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Protein, Whose Fold Resembles A Tim-Barrel Protein, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Forouhar, Y. Chen, J. Benach, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of Putative Vitamin-B12 Independent Methionine Synthase From Listeria Monocytogenes, Northeast Structural Genomics Target Lmr13
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE VITAMIN-B12 INDEPENDENT METHIONINE SYNTHASE FAMILY PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21
    Expression System StrainBL21(DE3)+MAGIC
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Gene985330
    Organism ScientificLISTERIA MONOCYTOGENES
    Organism Taxid169963
    StrainEGD-E

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:252 , TYR A:273 , PHE A:281 , ALA A:282 , LEU A:284 , LYS A:285 , HOH A:406BINDING SITE FOR RESIDUE PO4 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YPX)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YPX)

(-) 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:318
 aligned with Q8Y8Q1_LISMO | Q8Y8Q1 from UniProtKB/TrEMBL  Length:367

    Alignment length:366
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      
         Q8Y8Q1_LISMO     2 NQVAPFYADHVGSILRTKGIKDAREKFQSGEITALELRKIENTEIKYIVEKQKEVGLKSITDGEFRRAWWHFDFLENLDGVEGYDAAGGIQFSKVQTKSHSVKITGPIDFTTHPFIEDFIFLKEAVGDNHVAKQTIPSPAMLHYRGDIEYQPYLDDAEKFANDLATAYQKAIQAFYDAGCRYLQLDDTSWSYLCSDEQREVVRQRGFDPETLQETYKNLINEAIKHKPADMVITMHICRGNFRSTWIAEGGYGPVAETLFGKLNIDGFFLEYDNERSGDFAPLKYVTRPDLKIVLGLITSKTGELEDEAAIKARIEEASEIVPLSQLRLSPQCGFASTEEGNILTEEEQWDKLRYVVRLANDIWGE 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1ypxA00 A:2-367  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -----Meth_synt_2-1ypxA01 A:7-362                                                                                                                                                                                                                                                                                                                                         ----- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..ee.......--.hhhhhh..eeee..----------------.eeeeeeee....hhhhhhhhhhhhhh...ee.eeee.hhhhhhheee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhh....--------.....hhhhhhhhhhhhhh.......eeeeee..----------...hhhhhhhhh.....eeeee.....---............eeeeeee......-..hhhhhhhhhhhhhhhhhh.eeeee.....--------hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ypx A   2 NQVAPFYADHVGSILRTKGIKDAREKFQSGEITALELRKIENTEIKYIVEKQKEVGLKSITDGEFRR--WHFDFLENLDGVEGY----------------SVKITGPIDFTTHPFIEDFIFLKEAVGDNHVAKQTIPSPAmLHYRGDIEYQPYLDDAEKFANDLATAYQKAIQAFYDAGCRYLQLDDTSWSYLCSDE--------GFDPETLQETYKNLINEAIKHKPADmVITmHICR----------GGYGPVAETLFGKLNIDGFFLEYDNER---FAPLKYVTRPDLKIVLGLITSKTGE-EDEAAIKARIEEASEIVPLSQLRLSPQCGFA--------TEEEQWDKLRYVVRLANDIWGE 367
                                    11        21        31        41        51        61      | 71        81   |     -         -|      111       121       131       141|      151       161       171       181       191      |  -     | 211       221       231|   |   |-       251       261       271     | 281       291       301   | | 311       321       331     |   -    |  351       361      
                                                                                             68 71            85              102                                     142-MSE                                                 198      207                      232-MSE 240        251                       277 281                     305 |                           337      346                     
                                                                                                                                                                                                                                                                    236-MSE                                                                307                                                            

   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 1YPX)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8Y8Q1_LISMO | Q8Y8Q1)
molecular function
    GO:0003871    5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity    Catalysis of the reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate.
    GO:0008705    methionine synthase activity    Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0050667    homocysteine metabolic process    The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
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.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ypx)
 

(-) 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
  1ypx
    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
  Q8Y8Q1_LISMO | Q8Y8Q1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q8Y8Q1_LISMO | Q8Y8Q1
    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 1YPX)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YPX)