Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 ASPARAGINE OXYGENASE IN COMPLEX WITH FE(II)
 
Authors :  L. -O. Essen, M. Strieker
Date :  05 Jan 07  (Deposition) - 06 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A
Keywords :  Nonribosomal Peptide Synthesis; Non-Heme Iron(Ii); Alpha- Ketoglutarate Oxygenase; Beta-Hydroxylated Amino Acid, Oxidoreductase, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Strieker, F. Kopp, C. Mahlert, L. -O. Essen, M. A. Marahiel
Mechanistic And Structural Basis Of Stereospecific Cbeta-Hydroxylation In Calcium-Dependent Antibiotic, A Daptomycin-Type Lipopeptide
Acs Chem. Biol. V. 2 187 2007
PubMed-ID: 17373765  |  Reference-DOI: 10.1021/CB700012Y

(-) Compounds

Molecule 1 - ASPARAGINE OXYGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PQTEVMS01
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SCO3236 (ASNO)
    Organism Scientific: STREPTOMYCES COELICOLOR A3(2)
    Organism Taxid: 100226
    Other Details: EXPRESSION PLASMID ENCODES FOR N-TERMINAL HIS-7-TAG FOR IMAC
    Strain: DSMZ 40783
    Synonym: PUTATIVE OXYGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FE21Ligand/IonFE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:155 , GLU A:157 , HIS A:287 , HOH A:9072 , HOH A:9084 , HOH A:9091BINDING SITE FOR RESIDUE FE2 A 5001
2AC2SOFTWAREHIS A:270 , LEU A:272 , ARG A:301BINDING SITE FOR RESIDUE CL A 7001
3AC3SOFTWAREARG A:67 , GLY A:115 , LEU A:116 , HOH A:9077BINDING SITE FOR RESIDUE CL A 9001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OG6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:329 -Pro A:330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OG6)

(-) Exons   (0, 0)

(no "Exon" information available for 2OG6)

(-) 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:323
 aligned with ASNO_STRCO | Q9Z4Z5 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:323
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329   
           ASNO_STRCO    10 SRYDVTLDQSDAELVEEIAWKLATQATGRPDDAEWVEAARNAWHAWPATLRRDLAGFRRDSGPDGAIVLRGLPVDSMGLPPTPRVNGSVQREASLGAAVLLMTACGLGDPGAFLPEKNGALVQDVVPVPGMEEFQGNAGSTLLTFHNENAFHEHRPDFVMLLCLRADPTGRAGLRTACVRRVLPLLSDSTVDALWAPEFRTAPPPSFQLSGPEEAPAPVLLGDRSDPDLRVDLAATEPVTERAAEALRELQAHFDATAVTHRLLPGELAIVDNRVTVHGRTEFTPRYDGTDRWLQRTFVLTDLRRSRAMRPADGYVLGAAPQP 332
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------TauD-2og6A01 A:32-307                                                                                                                                                                                                                                                               ------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....eeeee.......................hhhhhhhhhhhhhhheeeee..hhhhh..eee.................eeee...........eeeeeeee........eeeeehhhhhhhhhhhhhhhhhh..ee...hhhhh...........eee....eee.......ee.hhhhhhhhhhhhhhhhhhheee.....eeeeee...eeeee............eeeeeeee.hhhhhhhhhhhhh.ee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2og6 A  10 SRYDVTLDQSDAELVEEIAWKLATQATGRPDDAEWVEAARNAWHAWPATLRRDLAGFRRDSGPDGAIVLRGLPVDSMGLPPTPRVNGSVQREASLGAAVLLMTACGLGDPGAFLPEKNGALVQDVVPVPGMEEFQGNAGSTLLTFHNENAFHEHRPDFVMLLCLRADPTGRAGLRTACVRRVLPLLSDSTVDALWAPEFRTAPPPSFQLSGPEEAPAPVLLGDRSDPDLRVDLAATEPVTERAAEALRELQAHFDATAVTHRLLPGELAIVDNRVTVHGRTEFTPRYDGTDRWLQRTFVLTDLRRSRAMRPADGYVLGAAPQP 332
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
   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 2OG6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OG6)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ASNO_STRCO | Q9Z4Z5)
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: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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:329 - Pro A:330   [ 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
  2og6
    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
  ASNO_STRCO | Q9Z4Z5
    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
  ASNO_STRCO | Q9Z4Z5
    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
        ASNO_STRCO | Q9Z4Z5: 2og5 2og7

(-) Related Entries Specified in the PDB File

2og5 APO FORM OF ASPARAGINE OXYGENASE
2og7 ASPARAGINE OXYGENASE WITH FE(II), 2S,3S-3-HYDROXYASPARAGINE AND SUCCINATE