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

(-) Description

Title :  CRYSTAL ANALYSIS OF CHORISMATE MUTASE FROM THERMUS THERMOPHILUS.
 
Authors :  E. Inagaki, M. Miyano, T. H. Tahirov
Date :  18 Feb 03  (Deposition) - 27 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Isomerase, Chorismate Mutase, Shikimate Pathway, Mutant, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Inagaki, S. Kuramitsu, S. Yokoyama, M. Miyano, T. H. Tahirov
The Crystal Structure Of Chorismate Mutase From Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CHORISMATE MUTASE
    Chains: A, B, C
    EC Number: 5.4.99.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Other Details: MUTATION OF PHE 55 TO SER
    Strain: HB8

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ODE)

(-) Sites  (0, 0)

(no "Site" information available for 1ODE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHORISMATE_MUT_1PS51167 Chorismate mutase domain profile.AROH_THETH2-120
 
 		  3A:2-117
B:2-116
C:2-116

(-) Exons   (0, 0)

(no "Exon" information available for 1ODE)

(-) 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:117
 aligned with AROH_THETH | Q84FH6 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           AROH_THETH     1 MVRGIRGAITVEEDTPEAIHQATRELLLKMLEANGIQSYEELAAVIFTVTEDLTSAFPAEAARQIGMHRVPLLSAREVPVPGSLPRVIRVLALWNTDTPQDRVRHVYLREAVRLRPD 117
               SCOP domains d1odea_ A: Chorismate mutase                                                                                          SCOP domains
               CATH domains 1odeA00 A:1-117  [code=3.30.1330.40, no name defined]                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee........hhhhhhhh......eeeee..........eeeeeeeee...hhhhh..ee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CHORISMATE_MUT_1  PDB: A:2-117 UniProt: 2-120                                                                        PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1ode A   1 MVRGIRGAITVEEDTPEAIHQATRELLLKMLEANGIQSYEELAAVIFTVTEDLTSAFPAEAARQIGMHRVPLLSAREVPVPGSLPRVIRVLALWNTDTPQDRVRHVYLREAVRLRPD 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with AROH_THETH | Q84FH6 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
           AROH_THETH     1 MVRGIRGAITVEEDTPEAIHQATRELLLKMLEANGIQSYEELAAVIFTVTEDLTSAFPAEAARQIGMHRVPLLSAREVPVPGSLPRVIRVLALWNTDTPQDRVRHVYLREAVRLRP 116
               SCOP domains d1odeb_ B: Chorismate mutase                                                                                         SCOP domains
               CATH domains 1odeB00 B:1-116  [code=3.30.1330.40, no name defined]                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee........hhhhhhhh......eeeee..........eeeeeeeee...hhhhh..eeehhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CHORISMATE_MUT_1  PDB: B:2-116 UniProt: 2-120                                                                       PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1ode B   1 MVRGIRGAITVEEDTPEAIHQATRELLLKMLEANGIQSYEELAAVIFTVTEDLTSAFPAEAARQIGMHRVPLLSAREVPVPGSLPRVIRVLALWNTDTPQDRVRHVYLREAVRLRP 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain C from PDB  Type:PROTEIN  Length:116
 aligned with AROH_THETH | Q84FH6 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
           AROH_THETH     1 MVRGIRGAITVEEDTPEAIHQATRELLLKMLEANGIQSYEELAAVIFTVTEDLTSAFPAEAARQIGMHRVPLLSAREVPVPGSLPRVIRVLALWNTDTPQDRVRHVYLREAVRLRP 116
               SCOP domains d1odec_ C: Chorismate mutase                                                                                         SCOP domains
               CATH domains 1odeC00 C:1-116  [code=3.30.1330.40, no name defined]                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhhhhhhhhh.......eeeeeeee........hhhhhhhh......eeeee..........eeeeeeeee...hhhhh..ee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CHORISMATE_MUT_1  PDB: C:2-116 UniProt: 2-120                                                                       PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1ode C   1 MVRGIRGAITVEEDTPEAIHQATRELLLKMLEANGIQSYEELAAVIFTVTEDLTSAFPAEAARQIGMHRVPLLSAREVPVPGSLPRVIRVLALWNTDTPQDRVRHVYLREAVRLRP 116
                                    10        20        30        40        50        60        70        80        90       100       110
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (AROH_THETH | Q84FH6)
molecular function
    GO:0004106    chorismate mutase activity    Catalysis of the reaction: chorismate = prephenate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0046417    chorismate metabolic process    The chemical reactions and pathways involving chorismate, the anion of (3R-trans)-3-((1-carboxyethenyl)oxy)-4-hydroxy-1,5-cyclohexadiene-1-carboxylic acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
(no "Ligands, Modified Residues, Ions" information available for 1ode)
 
  Sites
(no "Sites" information available for 1ode)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ode)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ode
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AROH_THETH | Q84FH6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.4.99.5
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AROH_THETH | Q84FH6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AROH_THETH | Q84FH6: 1ufy 1ui9 4nwo

(-) Related Entries Specified in the PDB File

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