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(-) Description

Title :  ISOPENICILLIN N SYNTHASE WITH A 2-THIABICYCLOHEPTAN-6-ONE PRODUCT ANALOGUE
 
Authors :  A. C. Stewart, I. J. Clifton, R. M. Adlington, J. E. Baldwin, P. J. Rutledge
Date :  01 Dec 06  (Deposition) - 16 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Antibiotic Biosynthesis, Penicillin Biosynthesis, Iron, Oxygenase, Vitamin C, Metal-Binding, Oxidoreductase, B-Lactam Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Stewart, I. J. Clifton, R. M. Adlington, J. E. Baldwin, P. J. Rutledge
A Cyclobutanone Analogue Mimics Penicillin In Binding To Isopenicillin N Synthase.
Chembiochem V. 8 2003 2007
PubMed-ID: 17907118  |  Reference-DOI: 10.1002/CBIC.200700176
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISOPENICILLIN N SYNTHETASE
    Chains: A
    EC Number: 1.21.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJB703
    Expression System Strain: NM554
    Expression System Taxid: 562
    Organism Scientific: EMERICELLA NIDULANS
    Organism Taxid: 162425
    Synonym: IPNS, ISOPENICILLIN N SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1A141Ligand/Ion(1S,4S,5S,7R)-7-{[(5S)-5-AMINO-5-CARBOXYPENTANOYL]AMINO}-3,3-DIMETHYL-6-OXO-2-THIABICYCLO[3.2.0]HEPTANE-4-CARBOXYLIC ACID
2FE1Ligand/IonFE (III) ION
3GOL1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:87 , TYR A:91 , SER A:183 , ILE A:187 , TYR A:189 , PHE A:211 , VAL A:272 , SER A:281 , FE A:1333 , HOH A:2285 , HOH A:2349 , HOH A:2388 , HOH A:2389 , HOH A:2390 , HOH A:2391 , HOH A:2393BINDING SITE FOR RESIDUE A14 A1332
2AC2SOFTWAREHIS A:214 , ASP A:216 , HIS A:270 , A14 A:1332 , HOH A:2285 , HOH A:2289BINDING SITE FOR RESIDUE FE A1333
3AC3SOFTWAREARG A:27 , LYS A:80 , HOH A:2394BINDING SITE FOR RESIDUE SO4 A1334
4AC4SOFTWAREALA A:204 , ASP A:205 , GLY A:206 , GLU A:215 , ALA A:258 , ARG A:308 , HOH A:2395 , HOH A:2396BINDING SITE FOR RESIDUE GOL A1335
5AC5SOFTWAREARG A:53 , ASP A:140 , PHE A:141 , HOH A:2203 , HOH A:2397 , HOH A:2398 , HOH A:2399 , HOH A:2400 , HOH A:2401 , HOH A:2402 , HOH A:2403BINDING SITE FOR RESIDUE SO4 A1336

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JB4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:193 -Pro A:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JB4)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IPNS_1PS00185 Isopenicillin N synthase signature 1.IPNS_EMENI97-106  1A:97-106
2FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.IPNS_EMENI176-288  1A:176-288
3IPNS_2PS00186 Isopenicillin N synthase signature 2.IPNS_EMENI250-263  1A:250-263

(-) Exons   (0, 0)

(no "Exon" information available for 2JB4)

(-) 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:329
 aligned with IPNS_EMENI | P05326 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:329
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322         
           IPNS_EMENI     3 SVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT 331
               SCOP domains d2jb4a_ A: automated matches                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2jb4A00 A:3-331 B-lactam Antibiotic, Isopenicillin N Synthase; Chain                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------DIOX_N-2jb4A02 A:9-132                                                                                                      ------------------------------------------------2OG-FeII_Oxy-2jb4A01 A:181-288                                                                              ------------------------------------------- Pfam domains
         Sec.struct. author ........eee.hhhhh.hhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh..............eee.........eeeee........hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.......eeeeeee......hhhhhee.....eeeeeee.....eeeeee.....eeeee..eeee.......eeeeehhhhhhhh........eeee.....eeeeeeee.........................hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------IPNS_1    ---------------------------------------------------------------------FE2OG_OXY  PDB: A:176-288 UniProt: 176-288                                                                       ------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IPNS_2        -------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jb4 A   3 SVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT 331
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
   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: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)
(-)
Clan: no clan defined [family: DIOX_N] (24)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IPNS_EMENI | P05326)
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:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0016216    isopenicillin-N synthase activity    Catalysis of the reaction: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + O(2) = 2 H(2)O + isopenicillin N.
    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: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.
    GO:0042318    penicillin biosynthetic process    The chemical reactions and pathways resulting in the formation of any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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  2jb4
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  IPNS_EMENI | P05326
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  1.21.3.1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IPNS_EMENI | P05326: 1bk0 1blz 1hb1 1hb2 1hb3 1hb4 1ips 1obn 1oc1 1odm 1odn 1qiq 1qje 1qjf 1uzw 1w03 1w04 1w05 1w06 1w3v 1w3x 2bjs 2bu9 2ivi 2ivj 2vau 2vbb 2vbd 2vbp 2vcm 2ve1 2wo7 2y60 2y6f 3zku 3zky 3zoi 4bb3

(-) Related Entries Specified in the PDB File

1bk0 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV-FE COMPLEX)
1blz ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV-FE-NO COMPLEX)
1hb1 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBIC ACOV FE COMPLEX)
1hb2 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)
1hb3 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)
1hb4 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)
1ips ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MANGANESE COMPLEX)
1obn ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL -AMINOBUTYRATE-FE-NO COMPLEX
1oc1 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL -AMINOBUTYRATE-FE COMPLEX
1odm ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBIC AC-VINYLGLYCINE FE COMPLEX )
1odn ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN-EXPOSED PRODUCT FROM ANAEROBIC AC-VINYLGLYCINE FE COMPLEX)
1qiq ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACMC FE COMPLEX)
1qje ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (IPN - FE COMPLEX)
1qjf ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MONOCYCLIC SULFOXIDE - FE COMPLEX)
1uzw ISOPENICILLIN N SYNTHASE WITH L-D-(A- AMINOADIPOYL)-L-CYSTEINYL-D-ISODEHYDROVALINE
1w03 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL -GLYCINE-FE COMPLEX
1w04 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL -GLYCINE-FE-NO COMPLEX
1w05 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL -ALANINE-FE COMPLEX
1w06 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL -ALANINE-FE NO COMPLEX
1w3v ISOPENICILLIN N SYNTHASE D-(L-A-AMINOADIPOYL )-(3R)-METHYL-L-CYSTEINE D-A- HYDROXYISOVALERYL ESTER COMPLEX (ANAEROBIC)
1w3x ISOPENICILLIN N SYNTHASE D-(L-A-AMINOADIPOYL )-(3R)-METHYL-L-CYSTEINE D-A- HYDROXYISOVALERYL ESTER COMPLEX (OXYGEN EXPOSED 5 MINUTES 20 BAR)
2bjs ISOPENICILLIN N SYNTHASE C-TERMINAL TRUNCATION MUTANT
2bu9 ISOPENICILLIN N SYNTHASE COMPLEXED WITH L- AMINOADIPOYL-L-CYSTEINYL-L-HEXAFLUOROVALINE
2ivi ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBIC AC-METHYL-CYCLOPROPYLGLYCINE FE COMPLEX)
2ivj ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBIC AC-CYCLOPROPYLGLYCINE FE COMPLEX)