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(-) Description

Title :  CRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT D38N FROM PSEUDOMONAS TESTOSTERONI COMPLEXED WITH 5ALPHA-ESTRAN-3,17-DIONE
 
Authors :  M. Byun, M. -S. Kim, B. -H. Oh
Date :  29 May 03  (Deposition) - 31 Mar 05  (Release) - 09 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Isomerase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Byun, M. -S. Kim, B. -H. Oh
Crystal Structure Of 5-3-Ketosteroid Isomerase Mutant D38N From Pseudomonas Testosteroni Complexed With 5Alpha-Estran-3, 17-Dione
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - STEROID DELTA-ISOMERASE
    Chains: A, B, C, D
    EC Number: 5.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: PSEUDOMONAS TESTOSTERONI
    Organism Taxid: 285
    Synonym: DELTA-5-3-KETOSTEROID ISOMERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ESR4Ligand/Ion5-ALPHA-ESTRAN-3,17-DIONE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ESR2Ligand/Ion5-ALPHA-ESTRAN-3,17-DIONE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ESR2Ligand/Ion5-ALPHA-ESTRAN-3,17-DIONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:14 , ASN A:38 , PHE A:82 , PHE A:86 , VAL A:95 , PRO A:97 , ASP A:99 , MET A:112 , PHE A:116 , HOH A:2132BINDING SITE FOR RESIDUE ESR A1126
2AC2SOFTWARETYR B:288 , VAL B:295 , PHE B:316 , ILE B:321BINDING SITE FOR RESIDUE ESR B1326
3AC3SOFTWARETYR C:14 , ASN C:38 , SER C:58 , PHE C:86 , ASP C:99 , PHE C:116BINDING SITE FOR RESIDUE ESR C1126
4AC4SOFTWARETYR D:214 , ASN D:238 , SER D:258 , PHE D:286 , ASP D:299 , PHE D:316BINDING SITE FOR RESIDUE ESR D1326

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:38 -Pro A:39
2Asn B:238 -Pro B:239
3Asn C:38 -Pro C:39
4Asn D:238 -Pro D:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OHP)

(-) Exons   (0, 0)

(no "Exon" information available for 1OHP)

(-) Sequences/Alignments

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:125
 aligned with SDIS_COMTE | P00947 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           SDIS_COMTE     1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
               SCOP domains d1ohpa_ A: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                      SCOP domains
               CATH domains 1ohpA00 A:1-125  [code=3.10.450.50, no name defined]                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.......eehhhhhhhhhhhhh....eeee....eee..eeeeeeeeeeee.........eeeeee.....eeeeeee.hhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ohp A   1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVENPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFIVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with SDIS_COMTE | P00947 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           SDIS_COMTE     1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
               SCOP domains d1ohpb_ B: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                      SCOP domains
               CATH domains 1ohpB00 B:201-325  [code=3.10.450.50, no name defined]                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.......eehhhhhhhhhhhhh....eeee....eee..eeeeeeeeeee..........eeeeee.....eeeeeee.hhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ohp B 201 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVENPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFIVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 325
                                   210       220       230       240       250       260       270       280       290       300       310       320     


Chain C from PDB  Type:PROTEIN  Length:125
 aligned with SDIS_COMTE | P00947 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           SDIS_COMTE     1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
               SCOP domains d1ohpc_ C: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                      SCOP domains
               CATH domains 1ohpC00 C:1-125  [code=3.10.450.50, no name defined]                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.......eehhhhhhhhhhhhh....eeee....eee..eeeeeeeeeeee.........eeeeee.....eeeeeee.hhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ohp C   1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVENPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFIVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     


Chain D from PDB  Type:PROTEIN  Length:125
 aligned with SDIS_COMTE | P00947 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           SDIS_COMTE     1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 125
               SCOP domains d1ohpd_ D: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                      SCOP domains
               CATH domains 1ohpD00 D:201-325  [code=3.10.450.50, no name defined]                                                                        CATH domains
           Pfam domains (1) -----NTF2-1ohpD01 D:206-324                                                                                                 - Pfam domains (1)
           Pfam domains (2) -----NTF2-1ohpD02 D:206-324                                                                                                 - Pfam domains (2)
           Pfam domains (3) -----NTF2-1ohpD03 D:206-324                                                                                                 - Pfam domains (3)
           Pfam domains (4) -----NTF2-1ohpD04 D:206-324                                                                                                 - Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.......eehhhhhhhhhhhhh....eeee....eee..eeeeeeeeeeee..eeeee..eeeeee.....eeeeeee.hhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ohp D 201 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVENPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFIVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA 325
                                   210       220       230       240       250       260       270       280       290       300       310       320
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NTF2 (66)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SDIS_COMTE | P00947)
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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SDIS_COMTE | P00947: 1buq 1isk 1ocv 1ogz 1ohs 1qjg 3m8c 3mhe 3mki 3myt 3nbr 3nhx 3nm2 3nuv 3nxj 3ov4 3t8u 3unl 4l7k 5dre 8cho

(-) Related Entries Specified in the PDB File

1buq SOLUTION STRUCTURE OF DELTA-5-3-KETOSTEROID ISOMERASE COMPLEXED WITH THE STEROID 19- NORTESTOSTERONE-HEMISUCCINATE
1isk 3-OXO-DELTA5-STEROID ISOMERASE, NMR, 20 STRUCTURES
1ocv THE F116W MUTANT STRUCTURE OF KETOSTEROID ISOMERASE FROM COMAMONAS TESTOSTERONI
1ogz CRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANTS P39A COMPLEXED WITH EQUILENIN FROM PSEUDOMONAS TESTOSTERONI
1ohs CRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT Y14F/D38N FROM PSEUDOMONAS TESTOSTERONI COMPLEXED WITH ANDROSTANEDIONE
1qjg CRYSTAL STRUCTURE OF DELTA5-3-KETOSTEROID ISOMERASE FROM PSEUDOMONAS TESTOSTERONI IN COMPLEX WITH EQUILENIN
8cho CRYSTAL STRUCTURE OF DELTA5-3-KETOSTEROID ISOMERASE FROM PSEUDOMONAS TESTOSTERONI