1UNB - JenaLib

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Title :   DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH 2-OXOGLUTARATE AND AMPICILLIN

Authors :   K. Valegard, A. C. Terwisscha Van Scheltinga, A. Dubus, L. M. Oster, G. Rhangino, J. Hajdu, I. Andersson

Date :   09 Sep 03 (Deposition) - 09 Jan 04 (Release) - 22 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

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	:	EXPANDASE, DAOCS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	AKG	1	Ligand/Ion	2-OXOGLUTARIC ACID
2	FE2	1	Ligand/Ion	FE (II) ION
3	PN1	1	Ligand/Ion	(2S,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID

Biological Unit 1 (3, 9)

No.	Name	Count	Type	Full Name
1	AKG	3	Ligand/Ion	2-OXOGLUTARIC ACID
2	FE2	3	Ligand/Ion	FE (II) ION
3	PN1	3	Ligand/Ion	(2S,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:183 , ASP A:185 , HIS A:243 , AKG A:1311 , PN1 A:1312 , HOH A:2114	BINDING SITE FOR RESIDUE FE2 A1310
2	AC2	SOFTWARE	ARG A:162 , MET A:180 , HIS A:183 , ASP A:185 , LEU A:204 , HIS A:243 , VAL A:245 , ARG A:258 , SER A:260 , PHE A:264 , ILE A:305 , FE2 A:1310 , HOH A:2114	BINDING SITE FOR RESIDUE AKG A1311
3	AC3	SOFTWARE	THR A:72 , MET A:73 , LEU A:158 , MET A:180 , HIS A:183 , ASP A:185 , ILE A:192 , HIS A:243 , VAL A:245 , VAL A:262 , PHE A:264 , ASN A:304 , FE2 A:1310 , HOH A:2108 , HOH A:2114	BINDING SITE FOR RESIDUE PN1 A1312

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

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

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE2OG_OXY	PS51471	Fe(2+) 2-oxoglutarate dioxygenase domain profile.	CEFE_STRC2	154-267	1	A:154-267
2	IPNS_2	PS00186	Isopenicillin N synthase signature 2.	CEFE_STRC2	223-236	1	A:223-236

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE2OG_OXY	PS51471	Fe(2+) 2-oxoglutarate dioxygenase domain profile.	CEFE_STRC2	154-267	3	A:154-267
2	IPNS_2	PS00186	Isopenicillin N synthase signature 2.	CEFE_STRC2	223-236	3	A:223-236

(no "Exon" information available for 1UNB)

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:289
 aligned with CEFE_STRC2 | P18548 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    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       310
           CEFE_STRC2     1 MDTTVPTFSLAELQQGLHQDEFRRCLRDKGLFYLTDCGLTDTELKSAKDLVIDFFEHGSEAEKRAVTSPVPTMRRGFTGLESESTAQITNTGSYSDYSMCYSMGTADNLFPSGDFERIWTQYFDRQYTASRAVAREVLRATGTEPDGGVEAFLDCEPLLRFRYFPQVPEHRSAEEQPLRMAPHYDLSMVTLIQQTPCANGFVSLQAEVGGAFTDLPYRPDAVLVFCGAIATLVTGGQVKAPRHHVAAPRRDQIAGSSRTSSVFFLRPNADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVNIRRTSK 310
               SCOP domains d1unba_ A: Deacetoxycephalosporin C synthase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1unbA00 A:1-310 B-lactam Antibiotic, Isopenicillin N Synthase; Chain                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeehhhhhh..hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeee.----------..hhhhh.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
                 1unb A   1 MDTTVPTFSLAELQQGLHQDEFRRCLRDKGLFYLTDCGLTDTELKSAKDLVIDFFEHGSEAEKRAVTSPVPTMRRGFTGL----------TGSYSDYSMCYSMGTADNLFPSGDFERIWTQYFDRQYTASRAVAREVLRATGTEPDGGVEAFLDCEPLLRFRYFPQ-----------LRMAPHYDLSMVTLIQQTPCANGFVSLQAEVGGAFTDLPYRPDAVLVFCGAIATLVTGGQVKAPRHHVAAPRRDQIAGSSRTSSVFFLRPNADFTFSVPLARECGFDVSLDGETATFQDWIGGNYVNIRRTSK 310
                                    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       300       310
                                                                                                          80         91                                                                        166         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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: Penicillin synthase-like (62)

Protein domain: Deacetoxycephalosporin C synthase (17)

Streptomyces clavuligerus [TaxId: 1901] (17)

d1unba_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

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

Streptomyces clavuligerus. Organism_taxid: 1901. (13)

1unbA00

A:1-310

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

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.

Asymmetric Unit
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Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1.14.20.1
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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
1uo9	DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH SUCCINATE
1uob	DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH 2-OXOGLUTARATE AND PENICILLIN G
1uof	DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH PENICILLIN G
1uog	DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH DEACETOXYCEPHALOSPORIN C

Description

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Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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