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(-) Description

Title :  CONFORMATIONAL FLEXIBILITY OF THE C-TERMINUS WITH IMPLICATIONS FOR SUBSTRATE BINDING AND CATALYSIS IN A NEW CRYSTAL FORM OF DEACETOXYCEPHALOSPORIN C SYNTHASE
 
Authors :  L. M. Oster, A. C. Terwisscha Van Scheltinga, K. Valegard, A. Mackenz A. Dubus, J. Hajdu, I. Andersson
Date :  30 Jun 04  (Deposition) - 30 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Cephalosporin, Penicillin, Mononuclear Ferrous Enzymes, 2-Oxoglutarate Dependent Oxygenases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Oster, A. C. Terwisscha Van Scheltinga, K. Valegard, A. Mackenzie Hose, A. Dubus, J. Hajdu, I. Andersson
Conformational Flexibility Of The C Terminus With Implications For Substrate Binding And Catalysis Revealed In A New Crystal Form Of Deacetoxycephalosporin C Synthase
J. Mol. Biol. V. 343 157 2004
PubMed-ID: 15381427  |  Reference-DOI: 10.1016/J.JMB.2004.07.049

(-) Compounds

Molecule 1 - DEACETOXYCEPHALOSPORIN C SYNTHASE
    Chains: A
    EC Number: 1.14.20.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Taxid: 562
    Organism Scientific: STREPTOMYCES CLAVULIGERUS
    Organism Taxid: 1901
    Synonym: DAOCS, EXPANDASE

 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 1W28)

(-) Sites  (0, 0)

(no "Site" information available for 1W28)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W28)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W28)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W28)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological 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

(-) Exons   (0, 0)

(no "Exon" information available for 1W28)

(-) 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:272
 aligned with CEFE_STRC2 | P18548 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:298
                                    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        
           CEFE_STRC2     1 MDTTVPTFSLAELQQGLHQDEFRRCLRDKGLFYLTDCGLTDTELKSAKDLVIDFFEHGSEAEKRAVTSPVPTMRRGFTGLESESTAQITNTGSYSDYSMCYSMGTADNLFPSGDFERIWTQYFDRQYTASRAVAREVLRATGTEPDGGVEAFLDCEPLLRFRYFPQVPEHRSAEEQPLRMAPHYDLSMVTLIQQTPCANGFVSLQAEVGGAFTDLPYRPDAVLVFCGAIATLVTGGQVKAPRHHVAAPRRDQIAGSSRTSSVFFLRPNADFTFSVPLARECGFDVSLDGETATFQDWI 298
               SCOP domains d1w28a_ A: Deacetoxycephalosporin C synthase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1w28A00 A:1-298 B-lactam Antibiotic, Isopenicillin N Synthase; Chain                                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeehhhhhh..hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee...---------------..eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh...eeeeeee..-----------...........eeeeeee........eeeee..eeee.......eeeeehhhhhhhh........eee...hhhhh....eeeeeeee......eeehhhhhhh.........eeehhhhh 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
                 1w28 A   1 MDTTVPTFSLAELQQGLHQDEFRRCLRDKGLFYLTDCGLTDTELKSAKDLVIDFFEHGSEAEKRAVTSPVPTMRRGFTGLE---------------YSMCYSMGTADNLFPSGDFERIWTQYFDRQYTASRAVAREVLRATGTEPDGGVEAFLDCEPLLRFRYFPQ-----------LRMAPHYDLSMVTLIQQTPCANGFVSLQAEVGGAFTDLPYRPDAVLVFCGAIATLVTGGQVKAPRHHVAAPRRDQIAGSSRTSSVFFLRPNADFTFSVPLARECGFDVSLDGETATFQDWI 298
                                    10        20        30        40        50        60        70        80|        -      |100       110       120       130       140       150       160     |   -       180       190       200       210       220       230       240       250       260       270       280       290        
                                                                                                           81              97                                                                  166         178
   Legend:   → Mismatch (orange background)
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  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: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1W28)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological 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.

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  1w28
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  CEFE_STRC2 | P18548
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  1.14.20.1
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 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 1uob 1uof 1uog 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 DEAXETYLCEPHALOSPORIN C SYNTHASE COMPLEXED WITH 2-OXOGLUTARATE AND AMPICILLIN
1uo9 DEAXETYLCEPHALOSPORIN C SYNTHASE COMPLEXED WITH SUCCINATE
1uob DEAXETYLCEPHALOSPORIN C SYNTHASE COMPLEXED WITH 2-OXOGLUTARATE AND PENICILLIN G
1uof DEAXETYLCEPHALOSPORIN C SYNTHASE COMPLEXED WITH PENICILLIN G
1uog DEAXETYLCEPHALOSPORIN C SYNTHASE COMPLEXED WITH DEACETOXYCEPHALOSPORIN C
1w2a DEACETOXYCEPHALOSPORIN C SYNTHASE (WITH HIS- TAG) COMPLEXED WITH FE(II) AND ETHYLENE GLYCOL
1w2n DEACETOXYCEPHALOSPORIN C SYNTHASE (WITH A N- TERMINAL HIS-TAG) IN COMPLEX WITH FE(II) AND AMPICILLIN
1w2o DEACETOXYCEPHALOSPORIN C SYNTHASE (WITH A N- TERMINAL HIS-TAG) IN COMPLEX WITH FE(II) AND DEACETOXYCEPHALOSPORIN C