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(-) Description

Title :  CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE D40N FROM PSEUDOMONAS PUTIDA (PKSI) WITH BOUND 3-FLUORO-4-NITROPHENOL
 
Authors :  J. M. M. Caaveiro, B. Pybus, D. Ringe, G. A. Petsko, P. A. Sigala
Date :  16 Aug 11  (Deposition) - 22 Aug 12  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrogen Bond, Ksi, Enzyme Catalysis, Transition State, Oxyanion Hole, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Sigala, A. T. Fafarman, J. P. Schwans, S. D. Fried, T. D. Fenn, J. M. M. Caaveiro, B. Pybus, D. Ringe, G. A. Petsko, S. G. Boxer, D. Herschlag
Quantitative Dissection Of Hydrogen Bond-Mediated Proton Transfer In The Ketosteroid Isomerase Active Site
Proc. Natl. Acad. Sci. Usa V. 110 E2552 2013
PubMed-ID: 23798390  |  Reference-DOI: 10.1073/PNAS.1302191110

(-) Compounds

Molecule 1 - STEROID DELTA-ISOMERASE
    Chains: A, B
    EC Number: 5.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: KSI
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: DELTA(5)-3-KETOSTEROID ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FNN2Ligand/Ion3-FLUORO-4-NITROPHENOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:16 , ASN A:40 , PHE A:86 , VAL A:88 , ASP A:103 , MET A:116 , ALA A:118BINDING SITE FOR RESIDUE FNN A 140
2AC2SOFTWARETYR B:16 , ASN B:40 , PHE B:86 , ASP B:103 , MET B:116BINDING SITE FOR RESIDUE FNN B 140

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:40 -Pro A:41
2Asn B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VGN)

(-) Sequences/Alignments

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:127
 aligned with SDIS_PSEPU | P07445 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
           SDIS_PSEPU     1 MNLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
               SCOP domains d3vgna_ A: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhhh....eeee....ee....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vgn A   1 MNLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with SDIS_PSEPU | P07445 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
           SDIS_PSEPU     1 MNLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
               SCOP domains d3vgnb_ B: Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhhh...eeeee....ee....eeeeeeeeeee....eeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vgn B   1 MNLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVENPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
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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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SDIS_PSEPU | P07445: 1c7h 1cqs 1dmm 1dmn 1dmq 1e3r 1e3v 1e97 1ea2 1gs3 1k41 1ogx 1oh0 1oho 1opy 1vzz 1w00 1w01 1w02 1w6y 2inx 2pzv 3cpo 3fzw 3ipt 3ows 3owu 3owy 3ox9 3oxa 3rgr 3sed 3t8n 3vsy 4cdl 4k1u 4k1v 5ai1 5d81 5d82 5d83 5g2g 5kp1 5kp3 5kp4

(-) Related Entries Specified in the PDB File

2inx CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE D40N FROM PSEUDOMONAS PUTIDA (PKSI) WITH BOUND 2,6-DIFLUOROPHENOL
2pzw CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE D40N FROM PSEUDOMONAS PUTIDA (PKSI) WITH BOUND PHENOL
3cpo CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE D40N WITH BOUND 2-FLUOROPHENOL
3fzw CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE D40N-D103N FROM PSEUDOMONAS PUTIDA (PKSI) WITH BOUND EQUILENIN