1W3X - JenaLib

Title :   ISOPENICILLIN N SYNTHASE D-(L-A-AMINOADIPOYL)-(3R)-METHYL-L-CYSTEINE D-A-HYDROXYISOVALERYL ESTER COMPLEX (OXYGEN EXPOSED 5 MINUTES 20 BAR)

Authors :   A. Daruzzaman, I. J. Clifton, P. J. Rutledge

Date :   20 Jul 04 (Deposition) - 07 Dec 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.46

Chains :   Asym./Biol. Unit : A

Keywords :   Synthase, 3D-Structure, Antibiotic Biosynthesis, B-Lactam Antibiotic, Iron, Oxidoreductase, Oxygenase, Penicillin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Daruzzaman, I. J. Clifton, R. M. Adlington, J. E. Baldwin, P. J. Rutledge
Unexpected Oxidation Of A Depsipeptide Substrate Analogue In Crystalline Isopenicillin N Synthase.
Chembiochem V. 7 351 2006
PubMed-ID: 16444759 | Reference-DOI: 10.1002/CBIC.200500282

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

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 d1w3xa_ A: Isopenicillin N synthase                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1w3xA00 A:3-331 B-lactam Antibiotic, Isopenicillin N Synthase; Chain                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------DIOX_N-1w3xA02 A:9-132                                                                                                      ------------------------------------------------2OG-FeII_Oxy-1w3xA01 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
                 1w3x 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)

CATH Domains (1, 1)

Pfam Domains (2, 2)

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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	1w3x
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	1.21.3.1
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Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

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)
2bjs	ISOPENICILLIN N SYNTHASE C-TERMINAL TRUNCATION MUTANT
2bu9	ISOPENICILLIN N SYNTHASE COMPLEXED WITH L- AMINOADIPOYL-L-CYSTEINYL-L-HEXAFLUOROVALINE

Description