Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH 2-OXOGLUTARATE AND PENICILLIN G
 
Authors :  K. Valegard, A. C. Terwisscha Van Scheltinga, A. Dubus, L. M. Oster, G. Rhangino, J. Hajdu, I. Andersson
Date :  16 Sep 03  (Deposition) - 09 Jan 04  (Release) - 22 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Oxidoreductase, Antibiotic Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Valegard, A. C. Terwisscha Van Scheltinga, A. Dubus, G. Ranghino, L. M. Oster, J. Hajdu, I. Andersson
The Structural Basis Of Cephalosporin Formation In A Mononuclear Ferrous Enzyme
Nat. Struct. Mol. Biol. V. 11 95 2004
PubMed-ID: 14718929  |  Reference-DOI: 10.1038/NSMB712

(-) Compounds

Molecule 1 - DEACETOXYCEPHALOSPORIN C SYNTHETASE
    Chains: A
    EC Number: 1.14.20.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Organism Scientific: STREPTOMYCES CLAVULIGERUS
    Organism Taxid: 1901
    Synonym: DAOCS, EXPANDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2FE21Ligand/IonFE (II) ION
3PNN1Ligand/IonPENICILLIN G
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1AKG3Ligand/Ion2-OXOGLUTARIC ACID
2FE23Ligand/IonFE (II) ION
3PNN3Ligand/IonPENICILLIN G

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:73 , SER A:102 , LEU A:158 , MET A:180 , HIS A:183 , ASP A:185 , ILE A:192 , HIS A:243 , SER A:260 , VAL A:262 , PHE A:264 , FE2 A:1310 , HOH A:2090 , HOH A:2156BINDING SITE FOR RESIDUE PNN A1311
2AC2SOFTWAREHIS A:183 , ASP A:185 , HIS A:243 , PNN A:1311 , AKG A:1312 , HOH A:2090BINDING SITE FOR RESIDUE FE2 A1310
3AC3SOFTWAREARG A:162 , MET A:180 , HIS A:183 , ASP A:185 , LEU A:204 , HIS A:243 , ARG A:258 , SER A:260 , PHE A:264 , FE2 A:1310 , HOH A:2090BINDING SITE FOR RESIDUE AKG A1312

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.CEFE_STRC2154-267  1A:154-267
2IPNS_2PS00186 Isopenicillin N synthase signature 2.CEFE_STRC2223-236  1A:223-236
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.CEFE_STRC2154-267  3A:154-267
2IPNS_2PS00186 Isopenicillin N synthase signature 2.CEFE_STRC2223-236  3A:223-236

(-) Exons   (0, 0)

(no "Exon" information available for 1UOB)

(-) Sequences/Alignments

Asymmetric 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:282
 aligned with CEFE_STRC2 | P18548 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300         
           CEFE_STRC2     1 MDTTVPTFSLAELQQGLHQDEFRRCLRDKGLFYLTDCGLTDTELKSAKDLVIDFFEHGSEAEKRAVTSPVPTMRRGFTGLESESTAQITNTGSYSDYSMCYSMGTADNLFPSGDFERIWTQYFDRQYTASRAVAREVLRATGTEPDGGVEAFLDCEPLLRFRYFPQVPEHRSAEEQPLRMAPHYDLSMVTLIQQTPCANGFVSLQAEVGGAFTDLPYRPDAVLVFCGAIATLVTGGQVKAPRHHVAAPRRDQIAGSSRTSSVFFLRPNADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVNIRRTS 309
               SCOP domains d1uoba_ A: Deacetoxycephalosporin C synthase                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1uobA00 A:1-309 B-lactam Antibiotic, Isopenicillin N Synthase; Chain                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeehhhhhh..hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh..........eee.-----------------..eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh...eeeeeee...----------..eeeeee...eeeeeee........eeeee..eeee.......eeeeehhhhhhhh........eee............eeeeeeee......eeehhhhhhh.........eeehhhhhh.....ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------FE2OG_OXY  PDB: A:154-267 UniProt: 154-267                                                                        ------------------------------------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IPNS_2        ------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uob A   1 MDTTVPTFSLAELQQGLHQDEFRRCLRDKGLFYLTDCGLTDTELKSAKDLVIDFFEHGSEAEKRAVTSPVPTMRRGFTG-----------------YSMCYSMGTADNLFPSGDFERIWTQYFDRQYTASRAVAREVLRATGTEPDGGVEAFLDCEPLLRFRYFPQV----------LRMAPHYDLSMVTLIQQTPCANGFVSLQAEVGGAFTDLPYRPDAVLVFCGAIATLVTGGQVKAPRHHVAAPRRDQIAGSSRTSSVFFLRPNADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVNIRRTS 309
                                    10        20        30        40        50        60        70        |-         -      |100       110       120       130       140       150       160      |  -       180       190       200       210       220       230       240       250       260       270       280       290       300         
                                                                                                         79                97                                                                   167        178
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (CEFE_STRC2 | P18548)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0050599    deacetoxycephalosporin-C synthase activity    Catalysis of the reaction: 2-oxoglutarate + O(2) + penicillin N = CO(2) + deacetoxycephalosporin C + H(2)O + succinate.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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 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 ]
    PNN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1uob)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1uob
    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
  CEFE_STRC2 | P18548
    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)
  1.14.20.1
    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
  CEFE_STRC2 | P18548
    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
        CEFE_STRC2 | P18548: 1dcs 1e5h 1e5i 1hjf 1hjg 1rxf 1rxg 1unb 1uo9 1uof 1uog 1w28 1w2a 1w2n 1w2o 2jb8

(-) Related Entries Specified in the PDB File

1dcs DEACETOXYCEPHALOSPORIN C SYNTHASE FROM S. CLAVULIGERUS
1e5h DELTA-R307A DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH SUCCINATE AND CARBON DIOXIDE
1e5i DELTA-R306 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH IRON AND 2-OXOGLUTARATE.
1hjf ALTERATION OF THE CO-SUBSTRATE SELECTIVITY OF DEACETOXYCEPHALOSPORIN C SYNTHASE: THE ROLE OF ARGININE-258
1hjg ALTERATION OF THE CO-SUBSTRATE SELECTIVITY OF DEACETOXYCEPHALOSPORIN C SYNTHASE: THE ROLE OF ARGININE-258
1rxf DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH FE(II)
1rxg DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH FE(II) AND 2-OXOGLUTARATE
1unb DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH 2-OXOGLUTARATE AND AMPICILLIN
1uo9 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH SUCCINATE
1uof DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH PENICILLIN G
1uog DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH DEACETOXYCEPHALOSPORIN C