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Title :   CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE Y16S/D40N FROM PSEUDOMONAS PUTIDA WITH BOUND EQUILENIN

Authors :   T. D. Fenn, P. A. Sigala, D. Herschlag

Date :   18 Aug 09 (Deposition) - 12 Jan 10 (Release) - 28 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Enzyme-Ligand Complex, Protein Cavity, Isomerase, Lipid Metabolism, Steroid Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Kraut, P. A. Sigala, T. D. Fenn, D. Herschlag
Dissecting The Paradoxical Effects Of Hydrogen Bond Mutations In The Ketosteroid Isomerase Oxyanion Hole.
Proc. Natl. Acad. Sci. Usa V. 107 1960 2010
PubMed-ID: 20080683 | Reference-DOI: 10.1073/PNAS.0911168107

Molecule 1 - STEROID DELTA-ISOMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.3.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21C
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	KSI
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Synonym	:	DELTA(5)-3-KETOSTEROID ISOMERASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	EQU	4	Ligand/Ion	EQUILENIN

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	EQU	2	Ligand/Ion	EQUILENIN

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	EQU	2	Ligand/Ion	EQUILENIN

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:40 , PHE A:86 , MET A:90 , LEU A:99 , ASP A:103 , MET A:116 , TRP A:120 , HOH A:174	BINDING SITE FOR RESIDUE EQU A 1128
2	AC2	SOFTWARE	ASN B:40 , PHE B:86 , MET B:90 , LEU B:99 , ASP B:103 , MET B:116 , TRP B:120	BINDING SITE FOR RESIDUE EQU B 1128
3	AC3	SOFTWARE	ASN C:40 , PHE C:56 , PHE C:86 , MET C:90 , LEU C:99 , ASP C:103 , MET C:116 , TRP C:120	BINDING SITE FOR RESIDUE EQU C 1128
4	AC4	SOFTWARE	ASN D:40 , PHE D:86 , MET D:90 , ASP D:103 , MET D:116	BINDING SITE FOR RESIDUE EQU D 1128

(no "SS Bond" information available for 3IPT)

Asymmetric Unit

No.	Residues
1	Asn A:40	-	Pro A:41
2	Asn B:40	-	Pro B:41
3	Asn C:40	-	Pro C:41
4	Asn D:40	-	Pro D:41

(no "SAP(SNP)/Variant" information available for 3IPT)

(no "PROSITE Motif" information available for 3IPT)

(no "Exon" information available for 3IPT)

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:124
 aligned with SDIS_PSEPU | P07445 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           SDIS_PSEPU     2 NLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSVR 128
               SCOP domains d3ipta_ A: Delta-5-3-ketosteroid isomerase, steroid delta-is   omerase, KSI                                                     SCOP domains
               CATH domains 3iptA00 A:2-128  [code=3.10.450.50, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhh---..eeee....ee....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ipt A   2 NLPTAQEVQGLMARSIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGL---KVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSVR 128
                                    11        21        31        41        51        61   |    71        81        91       101       111       121       
                                                                                      61  65

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with SDIS_PSEPU | P07445 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           SDIS_PSEPU     2 NLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
               SCOP domains d3iptb_ B: Delta-5-3-ketosteroid isomerase, steroid delta-is   omerase, KSI                                                    SCOP domains
               CATH domains 3iptB00 B:2-127  [code=3.10.450.50, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhh---..eeee....ee....eeeeeeeeeee....eeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ipt B   2 NLPTAQEVQGLMARSIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGL---KVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    11        21        31        41        51        61   |    71        81        91       101       111       121      
                                                                                      61  65

Chain C from PDB  Type:PROTEIN  Length:123
 aligned with SDIS_PSEPU | P07445 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           SDIS_PSEPU     2 NLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
               SCOP domains d3iptc_ C: Delta-5-3-ketosteroid isomerase, steroid delta-is   omerase, KSI                                                    SCOP domains
               CATH domains 3iptC00 C:2-127  [code=3.10.450.50, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhh---..eeee....ee....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ipt C   2 NLPTAQEVQGLMARSIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGL---KVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    11        21        31        41        51        61   |    71        81        91       101       111       121      
                                                                                      61  65

Chain D from PDB  Type:PROTEIN  Length:123
 aligned with SDIS_PSEPU | P07445 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           SDIS_PSEPU     2 NLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
               SCOP domains d3iptd_ D: Delta-5-3-ketosteroid isomerase, steroid delta-is   omerase, KSI                                                    SCOP domains
               CATH domains 3iptD00 D:2-127  [code=3.10.450.50, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhh---..eeee....ee....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ipt D   2 NLPTAQEVQGLMARSIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGL---KVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    11        21        31        41        51        61   |    71        81        91       101       111       121      
                                                                                      61  65

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cystatin-like (403)

Superfamily: NTF2-like (231)

Family: Ketosteroid isomerase-like (62)

Protein domain: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI (58)

Pseudomonas putida [TaxId: 303] (37)

1a	d3ipta_	A:
1b	d3iptb_	B:
1c	d3iptc_	C:
1d	d3iptd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.50, no name defined] (113)

Pseudomonas putida. Organism_taxid: 303. (6)

1a	3iptA00	A:2-128
1b	3iptC00	C:2-127
1c	3iptD00	D:2-127
1d	3iptB00	B:2-127

(no "Pfam Domain" information available for 3IPT)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SDIS_PSEPU | P07445)

molecular function
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0004769	steroid delta-isomerase activity	Catalysis of the reaction: a 3-oxo-delta(5)-steroid = a 3-oxo-delta(4)-steroid.
biological process
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.

Asymmetric Unit
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	Cis Peptide Bonds
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		Asn C:40 - Pro C:41	[ RasMol ]
		Asn D:40 - Pro D:41	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3IPT)

Description

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Ligands, Modified Residues, Ions (1, 4)

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