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(-) Description

Title :  CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE D38HD99N FROM PSEUDOMONAS TESTOSTERONI (TKSI)
 
Authors :  A. Gonzalez, Y. Tsai, J. Schwans, F. Sunden, D. Herschlag
Date :  11 May 10  (Deposition) - 23 Nov 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (2x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Isomerase, Lipid Metabolism, Steroid Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Schwans, F. Sunden, A. Gonzalez, Y. Tsai, D. Herschlag
Crystal Structure Of Ketosteroid Isomerase D38Hd99N From Pseudomonas Testosteroni (Tksi)
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 Plasmid: PKK
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: KSI
    Mutation: YES
    Organism Common: PSEUDOMONAS TESTOSTERONI
    Organism Scientific: COMAMONAS TESTOSTERONI
    Organism Taxid: 285
    Strain: ATC 11996
    Synonym: DELTA(5)-3-KETOSTEROID ISOMERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (2x): ABCD
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric Unit (3, 22)
No.NameCountTypeFull Name
1EQU3Ligand/IonEQUILENIN
2GOL4Ligand/IonGLYCEROL
3SO415Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1EQU2Ligand/IonEQUILENIN
2GOL2Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1EQU1Ligand/IonEQUILENIN
2GOL2Ligand/IonGLYCEROL
3SO49Ligand/IonSULFATE ION
Biological Unit 3 (3, 44)
No.NameCountTypeFull Name
1EQU6Ligand/IonEQUILENIN
2GOL8Ligand/IonGLYCEROL
3SO430Ligand/IonSULFATE ION
Biological Unit 4 (3, 12)
No.NameCountTypeFull Name
1EQU1Ligand/IonEQUILENIN
2GOL2Ligand/IonGLYCEROL
3SO49Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:6 , ARG A:13BINDING SITE FOR RESIDUE SO4 A 126
02AC2SOFTWARETYR A:14 , HIS A:38 , VAL A:84 , PHE A:86 , VAL A:95 , PRO A:97 , ASN A:99 , PHE A:116 , TYR D:88 , GLN D:89 , ARG D:91 , HOH D:134BINDING SITE FOR RESIDUE EQU A 127
03AC3SOFTWAREGLN A:89 , TYR D:14 , PHE D:54 , SER D:58 , VAL D:84 , MET D:112 , HOH D:150BINDING SITE FOR RESIDUE GOL A 128
04AC4SOFTWAREHOH A:413 , HIS B:6 , ARG B:13 , HOH B:371BINDING SITE FOR RESIDUE SO4 B 126
05AC5SOFTWAREASN B:104 , GLY B:105 , HOH B:156BINDING SITE FOR RESIDUE SO4 B 127
06AC6SOFTWAREARG B:102 , SER B:111 , HOH B:416BINDING SITE FOR RESIDUE SO4 B 128
07AC7SOFTWAREGLN B:89 , HOH B:277 , TYR C:14 , LEU C:18 , HIS C:38 , PHE C:54 , VAL C:84 , PHE C:86 , ASN C:99 , MET C:112 , PHE C:116BINDING SITE FOR RESIDUE EQU B 129
08AC8SOFTWAREASN B:2 , PRO B:4 , ALA B:73 , VAL B:74 , ALA B:75 , HOH B:396 , HOH D:417BINDING SITE FOR RESIDUE GOL B 130
09AC9SOFTWAREARG C:45 , GLU C:53 , PHE C:54 , ASN C:57BINDING SITE FOR RESIDUE SO4 C 126
10BC1SOFTWAREARG B:91 , HOH B:400 , ARG C:91 , THR C:93 , ALA C:123 , HOH C:143BINDING SITE FOR RESIDUE SO4 C 127
11BC2SOFTWAREHIS C:122 , ALA C:123BINDING SITE FOR RESIDUE SO4 C 128
12BC3SOFTWAREHIS A:100 , HIS C:100 , ARG C:102 , ARG C:113BINDING SITE FOR RESIDUE SO4 C 129
13BC4SOFTWAREMET C:1 , ASN C:76BINDING SITE FOR RESIDUE SO4 C 130
14BC5SOFTWARETYR B:14 , HIS B:38 , PHE B:54 , PHE B:86 , VAL B:95 , ASN B:99 , PHE B:116 , TYR C:88 , GLN C:89 , ARG C:91 , HOH C:399BINDING SITE FOR RESIDUE EQU C 131
15BC6SOFTWAREASP C:24 , VAL C:27 , ALA C:28 , ARG C:52 , GLU D:43BINDING SITE FOR RESIDUE GOL C 132
16BC7SOFTWAREHIS D:6 , ARG D:13 , SO4 D:131 , GOL D:132 , HOH D:162BINDING SITE FOR RESIDUE SO4 D 126
17BC8SOFTWAREASN D:104 , GLY D:105 , HOH D:159BINDING SITE FOR RESIDUE SO4 D 127
18BC9SOFTWAREHIS D:122 , ALA D:123BINDING SITE FOR RESIDUE SO4 D 128
19CC1SOFTWAREARG B:113 , HIS D:100 , ARG D:102 , ARG D:113BINDING SITE FOR RESIDUE SO4 D 129
20CC2SOFTWAREMET D:1 , ASN D:76BINDING SITE FOR RESIDUE SO4 D 130
21CC3SOFTWAREALA D:9 , ARG D:13 , ASN D:19 , SO4 D:126 , HOH D:164 , HOH D:290BINDING SITE FOR RESIDUE SO4 D 131
22CC4SOFTWAREALA D:9 , ASN D:19 , LEU D:63 , ALA D:64 , VAL D:65 , SO4 D:126BINDING SITE FOR RESIDUE GOL D 132

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MYT)

(-) 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:124
 aligned with SDIS_COMTE | P00947 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
           SDIS_COMTE     1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAG 124
               SCOP domains d3myta_ A: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.......eehhhhhhhhhhhhh....eeee....eee..eeeeeeeeeeee..eeeee..eeeeee.....eeeeeee.hhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3myt A   1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEHPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPINHFRFNGAGKVVSMRALFGEKNIHAG 124
                                    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 d3mytb_ B: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeee.......eehhhhhhhhhhhhh....eeee....eee..eeeeeeeeeeee..eeeee..eeeeee.....eeeeeee.hhh.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3myt B   1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEHPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPINHFRFNGAGKVVSMRALFGEKNIHAGA 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     


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 d3mytc_ C: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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
                 3myt C   1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEHPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPINHFRFNGAGKVVSMRALFGEKNIHAGA 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     


Chain D from PDB  Type:PROTEIN  Length:124
 aligned with SDIS_COMTE | P00947 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
           SDIS_COMTE     1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAG 124
               SCOP domains d3mytd_ D: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeee.......eehhhhhhhhhhhhh....eeee....eee..eeeeeeeeeeee..eeeee..eeeeee.....eeeeeee.hhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3myt D   1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEHPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPINHFRFNGAGKVVSMRALFGEKNIHAG 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MYT)

(-) Pfam Domains  (0, 0)

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

(-) 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 1ohp 1ohs 1qjg 3m8c 3mhe 3mki 3nbr 3nhx 3nm2 3nuv 3nxj 3ov4 3t8u 3unl 4l7k 5dre 8cho

(-) Related Entries Specified in the PDB File

3m8c 3mhe 3mki