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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STREPTOMYCES EXFOLIATUS LIPASE AT 1.9A RESOLUTION: A MODEL FOR A FAMILY OF PLATELET-ACTIVATING FACTOR ACETYLHYDROLASES
 
Authors :  Y. Wei, Z. S. Derewenda
Date :  11 Jul 97  (Deposition) - 15 Jul 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serine Hydrolase, Lipase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Wei, L. Swenson, C. Castro, U. Derewenda, W. Minor, H. Arai, J. Aoki, K. Inoue, L. Servin-Gonzalez, Z. S. Derewenda
Structure Of A Microbial Homologue Of Mammalian Platelet-Activating Factor Acetylhydrolases: Streptomyces Exfoliatus Lipase At 1. 9 A Resolution.
Structure V. 6 511 1998
PubMed-ID: 9562561  |  Reference-DOI: 10.1016/S0969-2126(98)00052-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIPASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneSTREPTOMYCES EXFOLIATUS
    Expression System Taxid562
    GeneSTREPTOMYCES EXFOLIATUS
    Organism ScientificSTREPTOMYCES EXFOLIATUS
    Organism Taxid1905

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JFR)

(-) Sites  (0, 0)

(no "Site" information available for 1JFR)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:242 -A:258
2B:242 -B:258

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Cys A:242 -Pro A:243
2Cys A:258 -Pro A:259
3Cys B:242 -Pro B:243
4Cys B:258 -Pro B:259

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JFR)

(-) 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:260
 aligned with Q56008_STRSQ | Q56008 from UniProtKB/TrEMBL  Length:310

    Alignment length:260
                                    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
         Q56008_STRSQ    51 NPYERGPAPTNASIEASRGPYATSQTSVSSLVASGFGGGTIYYPTSTADGTFGAVVISPGFTAYQSSIAWLGPRLASQGFVVFTIDTNTTLDQPDSRGRQLLSALDYLTQRSSVRTRVDATRLGVMGHSMGGGGSLEAAKSRTSLKAAIPLTGWNTDKTWPELRTPTLVVGADGDTVAPVATHSKPFYESLPGSLDKAYLELRGASHFTPNTSDTTIAKYSISWLKRFIDSDTRYEQFLCPIPRPSLTIAEYRGTCPHTS 310
               SCOP domains d1jfra_ A: Lipase                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1jfrA00 A:3-262  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh.......eeeeee..........eeeeee.........eeeee......hhh.hhhhhhhhhh..eeeee........hhhhhhhhhhhhhhhhh....hhh.....eeeeeehhhhhhhhhhhhh.....eeeee...............eeeeee...........hhhhhhh......eeeeee......hhh...hhhhhhhhhhhhhhh...hhhhhh..........eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jfr A   3 NPYERGPAPTNASIEASRGPYATSQTSVSSLVASGFGGGTIYYPTSTADGTFGAVVISPGFTAYQSSIAWLGPRLASQGFVVFTIDTNTTLDQPDSRGRQLLSALDYLTQRSSVRTRVDATRLGVMGHSMGGGGSLEAAKSRTSLKAAIPLTGWNTDKTWPELRTPTLVVGADGDTVAPVATHSKPFYESLPGSLDKAYLELRGASHFTPNTSDTTIAKYSISWLKRFIDSDTRYEQFLCPIPRPSLTIAEYRGTCPHTS 262
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with Q56008_STRSQ | Q56008 from UniProtKB/TrEMBL  Length:310

    Alignment length:260
                                    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
         Q56008_STRSQ    51 NPYERGPAPTNASIEASRGPYATSQTSVSSLVASGFGGGTIYYPTSTADGTFGAVVISPGFTAYQSSIAWLGPRLASQGFVVFTIDTNTTLDQPDSRGRQLLSALDYLTQRSSVRTRVDATRLGVMGHSMGGGGSLEAAKSRTSLKAAIPLTGWNTDKTWPELRTPTLVVGADGDTVAPVATHSKPFYESLPGSLDKAYLELRGASHFTPNTSDTTIAKYSISWLKRFIDSDTRYEQFLCPIPRPSLTIAEYRGTCPHTS 310
               SCOP domains d1jfrb_ B: Lipase                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1jfrB00 B:3-262  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                CATH domains
           Pfam domains (1) -----------------------------------------------------Abhydrolase_5-1jfrB01 B:56-210                                                                                                                             ---------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------Abhydrolase_5-1jfrB02 B:56-210                                                                                                                             ---------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..........hhhhh.......eeeeee..........eeeeee.........eeeee......hhh.hhhhhhhhhh..eeeee........hhhhhhhhhhhhhhhhh....hhh.....eeeeeehhhhhhhhhhhhh.....eeeee...............eeeeee...........hhhhhhh......eeeeee......hhh...hhhhhhhhhhhhhhh...hhhhhhh.........eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jfr B   3 NPYERGPAPTNASIEASRGPYATSQTSVSSLVASGFGGGTIYYPTSTADGTFGAVVISPGFTAYQSSIAWLGPRLASQGFVVFTIDTNTTLDQPDSRGRQLLSALDYLTQRSSVRTRVDATRLGVMGHSMGGGGSLEAAKSRTSLKAAIPLTGWNTDKTWPELRTPTLVVGADGDTVAPVATHSKPFYESLPGSLDKAYLELRGASHFTPNTSDTTIAKYSISWLKRFIDSDTRYEQFLCPIPRPSLTIAEYRGTCPHTS 262
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q56008_STRSQ | Q56008)
molecular function
    GO:0003847    1-alkyl-2-acetylglycerophosphocholine esterase activity    Catalysis of the reaction: 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine + H2O = 1-alkyl-sn-glycero-3-phosphocholine + acetate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.

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    Cys A:242 - Pro A:243   [ RasMol ]  
    Cys A:258 - Pro A:259   [ RasMol ]  
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