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 CLAVAMINATE SYNTHASE IN COMPLEX WITH FE(II), 2-OXOGLUTARATE AND PROCLAVAMINIC ACID
 
Authors :  Z. H. Zhang, J. Ren, D. K. Stammers, J. E. Baldwin, K. Harlos, C. J. Schofi
Date :  06 Jan 00  (Deposition) - 06 Jul 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxygenase, Trifunctional Enzyme, Clavaminate Synthase 1, Oxidoreductase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, J. Ren, D. K. Stammers, J. E. Baldwin, K. Harlos, C. J. Schofield
Structural Origins Of The Selectivity Of The Trifunctional Oxygenase Clavaminic Acid Synthase.
Nat. Struct. Biol. V. 7 127 2000
PubMed-ID: 10655615  |  Reference-DOI: 10.1038/72398

(-) Compounds

Molecule 1 - CLAVAMINATE SYNTHASE 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CLAVAMINIC ACID SYNTHASE 1 (CAS1)
    Organism Scientific: STREPTOMYCES CLAVULIGERUS
    Organism Taxid: 1901
    Synonym: CLAVAMINIC ACID SYNTHASE 1, CAS1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2FE21Ligand/IonFE (II) ION
3PCV1Ligand/Ion5-AMINO-3-HYDROXY-2-(2-OXO-AZETIDIN-1-YL)-PENTANOICACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:114 , LEU A:132 , SER A:134 , HIS A:144 , GLU A:146 , MET A:147 , ASP A:202 , ARG A:297 , TYR A:299BINDING SITE FOR RESIDUE PCV A 327
2AC2SOFTWAREHIS A:144 , GLU A:146 , HIS A:279 , AKG A:326BINDING SITE FOR RESIDUE FE2 A 325
3AC3SOFTWARESER A:134 , LEU A:141 , HIS A:144 , GLU A:146 , LEU A:159 , THR A:172 , HIS A:279 , ARG A:281 , ARG A:293 , LEU A:295 , ARG A:297 , FE2 A:325 , HOH A:371BINDING SITE FOR RESIDUE AKG A 326

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:83 -Pro A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DRT)

(-) 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:315
 aligned with CAS1_STRC2 | Q05581 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    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   
           CAS1_STRC2     2 TSVDCTAYGPELRALAARLPRTPRADLYAFLDAAHTAAASLPGALATALDTFNAEGSEDGHLLLRGLPVEADADLPTTPSSTPAPEDRSLLTMEAMLGLVGRRLGLHTGYRELRSGTVYHDVYPSPGAHHLSSETSETLLEFHTEMAYHRLQPNYVMLACSRADHERTAATLVASVRKALPLLDERTRARLLDRRMPCCVDVAFRGGVDDPGAIAQVKPLYGDADDPFLGYDRELLAPEDPADKEAVAALSKALDEVTEAVYLEPGDLLIVDNFRTTHARTPFSPRWDGKDRWLHRVYIRTDRNGQLSGGERAGDVVAFTPRG 324
               SCOP domains d1drta_ A: Clavaminate synthase                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1drtA00 A:2-324 Clavaminate synthase-like                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeee.....hhhhh...............hhhhhhhhhhhhhhhee.ee..hhhhh..eee.................eeee...........eeeeeeee........eeeeehhhhhhhhhhhhhhhhh...ee...hhhhh--------..ee..ee......ee..........hhhhhhhhhhhhhhhhhhheee......eeeee...eeeee............eeeeeeee.hhhhh.........ee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1drt A   2 TSVDCTAYGPELRALAARLPRTPRADLYAFLDAAHTAAASLPGALATALDTFNAEGSEDGHLLLRGLPVEADADLPTTPSSTPAPEDRSLLTMEAMLGLVGRRLGLHTGYRELRSGTVYHDVYPSPGAHHLSSETSETLLEFHTEMAYHRLQPNYVMLACSRADHERTAATLVASVRKALPLLDERTRARLLDRRMPCCVDVAFR--------IAQVKPLYGDADDPFLGYDRELLAPEDPADKEAVAALSKALDEVTEAVYLEPGDLLIVDNFRTTHARTPFSPRWDGKDRWLHRVYIRTDRNGQLSGGERAGDVVAFTPRG 324
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    |    -   |   221       231       241       251       261       271       281       291       301       311       321   
                                                                                                                                                                                                                                      206      215
   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: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CAS1_STRC2 | Q05581)
molecular function
    GO:0033758    clavaminate synthase activity    Catalysis of the reactions: deoxyamidinoproclavaminate + 2-oxoglutarate + O2 = amidinoproclavaminate + succinate + CO2 + H2O; proclavaminate + 2-oxoglutarate + O2 = dihydroclavaminate + succinate + CO2 + 2 H2O; and dihydroclavaminate + 2-oxoglutarate + O2 = clavaminate + succinate + CO2 + 2 H2O.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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:0033050    clavulanic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of clavulanic acid, (2R,3Z,5R)-3-(2-hydroxyethylidene)-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid.
    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.

 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
    AKG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PCV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:83 - Pro A:84   [ 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 | Asym./Biol. Unit - sites 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
  1drt
    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
  CAS1_STRC2 | Q05581
    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
  CAS1_STRC2 | Q05581
    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
        CAS1_STRC2 | Q05581: 1dry 1ds0 1ds1 1gvg

(-) Related Entries Specified in the PDB File

1dry 1ds0 1ds1