1IPS - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MANGANESE COMPLEX)

Authors :   P. L. Roach, I. J. Clifton, V. Fulop, K. Harlos, G. J. Barton, J. Hajdu, I. Andersson, C. J. Schofield, J. E. Baldwin

Date :   21 Mar 97 (Deposition) - 25 Mar 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

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

Reference :   P. L. Roach, I. J. Clifton, V. Fulop, K. Harlos, G. J. Barton, J. Hajdu, I. Andersson, C. J. Schofield, J. E. Baldwin
Crystal Structure Of Isopenicillin N Synthase Is The First From A New Structural Family Of Enzymes.
Nature V. 375 700 1995
PubMed-ID: 7791906 | Reference-DOI: 10.1038/375700A0
(for further references see the PDB file header)

Molecule 1 - ISOPENICILLIN N SYNTHASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJB703
	Expression System Strain	:	NM554
	Expression System Taxid	:	562
	Gene	:	PCB C
	Organism Scientific	:	EMERICELLA NIDULANS
	Organism Taxid	:	162425

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MN	4	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:214 , ASP A:216 , HIS A:270 , GLN A:330 , HOH A:352 , HOH A:353	BINDING SITE FOR RESIDUE MN A 350
2	AC2	SOFTWARE	GLU A:81 , HIS A:82 , HOH A:354 , HOH A:355	BINDING SITE FOR RESIDUE MN A 351
3	AC3	SOFTWARE	HIS B:214 , ASP B:216 , HIS B:270 , GLN B:330 , HOH B:352 , HOH B:353	BINDING SITE FOR RESIDUE MN B 350
4	AC4	SOFTWARE	HIS B:82 , HOH B:354	BINDING SITE FOR RESIDUE MN B 351
5	SA	UNKNOWN	HIS A:214 , ASP A:216 , HIS A:270 , GLN A:330	ACTIVE SITE (MN BINDING), A CHAIN.
6	SB	UNKNOWN	HIS B:214 , ASP B:216 , HIS B:270 , GLN B:330	ACTIVE SITE (MN BINDING), B CHAIN.

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

Asymmetric/Biological Unit

No.	Residues
1	Asp A:193	-	Pro A:194
2	Asp B:193	-	Pro B:194

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IPNS_1	PS00185	Isopenicillin N synthase signature 1.	IPNS_EMENI	97-106	2	A:97-106 B:97-106
2	FE2OG_OXY	PS51471	Fe(2+) 2-oxoglutarate dioxygenase domain profile.	IPNS_EMENI	176-288	2	A:176-288 B:176-288
3	IPNS_2	PS00186	Isopenicillin N synthase signature 2.	IPNS_EMENI	250-263	2	A:250-263 B:250-263

(no "Exon" information available for 1IPS)

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:328
 aligned with IPNS_EMENI | P05326 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:328
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
           IPNS_EMENI     4 VSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT 331
               SCOP domains d1ipsa_ A: Isopenicillin N synthase                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1ipsA00 A:4-331 B-lactam Antibiotic, Isopenicillin N Synthase; Chain                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.hhhh...hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh..hhhhhhh...............eee.........eeeee.........hhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhh........eeeeeee.......hhh....................eeeeee.....eeeee..eeee.......eeeee.hhhhhh.........eee......eeeeeeee..........................hhhhhhhhhhh........ 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
                 1ips A   4 VSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT 331
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

Chain B from PDB  Type:PROTEIN  Length:328
 aligned with IPNS_EMENI | P05326 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:328
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
           IPNS_EMENI     4 VSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT 331
               SCOP domains d1ipsb_ B: Isopenicillin N synthase                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1ipsB00 B:4-331 B-lactam Antibiotic, Isopenicillin N Synthase; Chain                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.hhhh...hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..hhhhhhh...............eee.........eeeee.........hhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhh........hhh.........eeeeee.......hhh....................eeeeee.....eeeee..eeee.......eeeee.hhhhhh.........eee......eeeeeeee..........................hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------IPNS_1    ---------------------------------------------------------------------FE2OG_OXY  PDB: B:176-288 UniProt: 176-288                                                                       ------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IPNS_2        -------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ips B   4 VSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT 331
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: Penicillin synthase-like (62)

Protein domain: Isopenicillin N synthase (26)

Emericella nidulans [TaxId: 162425] (26)

1a	d1ipsa_	A:
1b	d1ipsb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: B-lactam Antibiotic, Isopenicillin N Synthase; Chain (59)

Emericella nidulans. Organism_taxid: 162425. (9)

1a	1ipsA00	A:4-331
1b	1ipsB00	B:4-331

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:193 - Pro A:194	[ RasMol ]
		Asp B:193 - Pro B:194	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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