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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LIPASE COMPLEXED WITH RC-(RP,SP)-1,2-DIOCTYLCARBAMOYL-GLYCERO-3-O-OCTYLPHOSPHONATE
 
Authors :  M. Nardini, D. A. Lang, K. Liebeton, K. -E. Jaeger, B. W. Dijkstra
Date :  02 May 00  (Deposition) - 18 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.54
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipase, Alpha-Beta Hydrolase Fold, Pseudomonas, Phosphonate Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nardini, D. A. Lang, K. Liebeton, K. E. Jaeger, B. W. Dijkstra
Crystal Structure Of Pseudomonas Aeruginosa Lipase In The Open Conformation. The Prototype For Family I. 1 Of Bacterial Lipases.
J. Biol. Chem. V. 275 31219 2000
PubMed-ID: 10893416  |  Reference-DOI: 10.1074/JBC.M003903200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACTONIZING LIPASE
    Chains: A
    EC Number: 3.1.1.3
    Engineered: YES
    Expression System: PSEUDOMONAS AERUGINOSA
    Expression System Plasmid: PEL11
    Expression System Strain: PAC1R
    Expression System Taxid: 287
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: TRIACYL-GLYCEROL LIPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2OCP1Ligand/IonOCTYL-PHOSPHINIC ACID 1,2-BIS-OCTYLCARBAMOYLOXY-ETHYLESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:209 , ASP A:253 , GLN A:257 , VAL A:258 , LEU A:261 , HOH A:470 , HOH A:483BINDING SITE FOR RESIDUE CA A 286
2AC2SOFTWAREGLY A:15 , MET A:16 , LEU A:17 , TYR A:27 , SER A:82 , HIS A:83 , SER A:112 , LEU A:159 , HIS A:251 , VAL A:258BINDING SITE FOR RESIDUE OCP A 382

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:183 -A:235

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:257 -Val A:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LIP_PSEAE_001 *K33QLIP_PSEAE  ---  ---AK7Q
2UniProtVAR_LIP_PSEAE_002 *V156ILIP_PSEAE  ---  ---AV130I
3UniProtVAR_LIP_PSEAE_003 *Q202HLIP_PSEAE  ---  ---AQ176H
4UniProtVAR_LIP_PSEAE_004 *I204VLIP_PSEAE  ---  ---AI178V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.LIP_PSEAE102-111  1A:76-85

(-) Exons   (0, 0)

(no "Exon" information available for 1EX9)

(-) 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:285
 aligned with LIP_PSEAE | P26876 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:285
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306     
            LIP_PSEAE    27 STYTQTKYPIVLAHGMLGFDNILGVDYWFGIPSALRRDGAQVYVTEVSQLDTSEVRGEQLLQQVEEIVALSGQPKVNLIGHSHGGPTIRYVAAVRPDLIASATSVGAPHKGSDTADFLRQIPPGSAGEAVLSGLVNSLGALISFLSSGSTGTQNSLGSLESLNSEGAARFNAKYPQGIPTSACGEGAYKVNGVSYYSWSGSSPLTNFLDPSDAFLGASSLTFKNGTANDGLVGTCSSHLGMVIRDNYRMNHLDEVNQVFGLTSLFETSPVSVYRQHANRLKNASL 311
               SCOP domains d1ex9a_ A: Lipase                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ex9A00 A:1-285  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.......ee..ee...hhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..............ee..eeeeee...........hhhhhhhhhhhhh..................ee.........hhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------Q--------------------------------------------------------------------------------------------------------------------------I---------------------------------------------H-V----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------LIPASE_SER-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ex9 A   1 STYTQTKYPIVLAHGMLGFDNILGVDYWFGIPSALRRDGAQVYVTEVSQLDTSEVRGEQLLQQVEEIVALSGQPKVNLIGHSHGGPTIRYVAAVRPDLIASATSVGAPHKGSDTADFLRQIPPGSAGEAVLSGLVNSLGALISFLSSGSTGTQNSLGSLESLNSEGAARFNAKYPQGIPTSACGEGAYKVNGVSYYSWSGSSPLTNFLDPSDAFLGASSLTFKNGTANDGLVGTCSSHLGMVIRDNYRMNHLDEVNQVFGLTSLFETSPVSVYRQHANRLKNASL 285
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EX9)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LIP_PSEAE | P26876)
molecular function
    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.
    GO:0016298    lipase activity    Catalysis of the hydrolysis of a lipid or phospholipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004806    triglyceride lipase activity    Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate.
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.
    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.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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