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 STRUCTURE OF THE AROMATASE/CYCLASE DOMAIN OF TCMN FROM STREPTOMYCES GLAUCESCENS
 
Authors :  B. D. Ames, T. P. Korman, T. N. Vu, S. C. Tsai
Date :  26 Sep 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyclase, Aromatase, Polyketide, Helix-Grip, Dehydratase, Anticancer, Antibiotic, Antibiotic Biosynthesis, Methyltransferase, Multifunctional Enzyme, Transferase, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Ames, T. P. Korman, W. Zhang, P. Smith, T. Vu, Y. Tang, S. C. Tsai
Crystal Structure And Functional Analysis Of Tetracenomycin Aro/Cyc: Implications For Cyclization Specificity Of Aromatic Polyketides.
Proc. Natl. Acad. Sci. Usa V. 105 5349 2008
PubMed-ID: 18388203  |  Reference-DOI: 10.1073/PNAS.0709223105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MULTIFUNCTIONAL CYCLASE-DEHYDRATASE-3-O-METHYL TRANSFERASE TCMN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: TCMN
    Organism Scientific: STREPTOMYCES GLAUCESCENS
    Organism Taxid: 1907

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2RER)

(-) Sites  (0, 0)

(no "Site" information available for 2RER)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RER)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:154 -Pro A:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RER)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RER)

(-) Exons   (0, 0)

(no "Exon" information available for 2RER)

(-) 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:155
 aligned with TCMN_STRGA | P16559 from UniProtKB/Swiss-Prot  Length:494

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
           TCMN_STRGA     1 MAARTDNSIVVNAPFELVWDVTNDIEAWPELFSEYAEAEILRQDGDGFDFRLKTRPDANGRVWEWVSHRVPDKGSRTVRAHRVETGPFAYMNLHWTYRAVAGGTEMRWVQEFDMKPGAPFDNAHMTAHLNTTTRANMERIKKIIEDRHREGQRTP 155
               SCOP domains d2rera1 A:1-155 Multifunctional enzyme TcmN, cyclase/aromatase domain                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------Polyketide_cyc-2rerA01 A:11-141                                                                                                    -------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee.........eeeeeeeee....eeeeee.....eeeeeeeeeeeee..eeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rer A   1 MAARTDNSIVVNAPFELVWDVTNDIEAWPELFSEYAEAEILRQDGDGFDFRLKTRPDANGRVWEWVSHRVPDKGSRTVRAHRVETGPFAYMNLHWTYRAVAGGTEMRWVQEFDMKPGAPFDNAHMTAHLNTTTRANMERIKKIIEDRHREGQRTP 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RER)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Bet_V_1_like (93)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TCMN_STRGA | P16559)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    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:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

 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 2rer)
 
  Sites
(no "Sites" information available for 2rer)
 
  Cis Peptide Bonds
    Thr A:154 - Pro A:155   [ RasMol ]  
 

(-) 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
  2rer
    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
  TCMN_STRGA | P16559
    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)
  (no 'Enzyme Classificator' available)
    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
  TCMN_STRGA | P16559
    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
        TCMN_STRGA | P16559: 2res 2rez 3tvq

(-) Related Entries Specified in the PDB File

2res 2rez