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(-) Description

Title :  BURKHOLDERIA CEPACIA LIPASE COMPLEXED WITH S-INHIBITOR
 
Authors :  M. Luic, Z. Stefanic
Date :  14 Nov 06  (Deposition) - 04 Dec 07  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Pseudomonas Cepacia Lipase, Racemic Sec Alcohols, Transition State (Ts) Analogue, Molecular Modelling, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Luic, Z. Stefanic, I. Ceilinger, M. Hodoscek, D. Janezic, T. Lenac, I. L. Asler, D. Sepac, S. Tomic
Combined X-Ray Diffraction And Qm/Mm Study Of The Burkholderia Cepacia Lipase-Catalyzed Secondary Alcohol Esterification
J. Phys. Chem. B V. 112 4876 2008
PubMed-ID: 18386861  |  Reference-DOI: 10.1021/JP077717U

(-) Compounds

Molecule 1 - LIPASE
    Chains: A
    EC Number: 3.1.1.3
    Organism Scientific: BURKHOLDERIA CEPACIA
    Organism Taxid: 292
    Other Details: THE ENZYME SOURCE WAS A COMMERCIAL PREPARATION OF PSEUDOMONAS (BURKHOLDERIA) CEPACIA LIPASE OBTAINED FROM AMANO PHARMACEUTICALS CO., NAGOYA, JAPAN.
    Synonym: TRIACYLGLYCEROL LIPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2NA1Ligand/IonSODIUM ION
3POT1Ligand/Ion(1S)-1-(PHENOXYMETHYL)PROPYL METHYLPHOSPHONOCHLORIDOATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:242 , ASP A:288 , GLN A:292 , VAL A:296 , HOH A:619 , HOH A:638BINDING SITE FOR RESIDUE CA A 613
2AC2SOFTWARETHR A:7 , HOH A:633 , HOH A:673 , HOH A:697 , HOH A:717BINDING SITE FOR RESIDUE NA A 614
3AC3SOFTWAREGLY A:16 , LEU A:17 , SER A:87 , GLN A:88 , SER A:117 , PHE A:119 , ALA A:120 , HIS A:286BINDING SITE FOR RESIDUE POT A 612

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:190 -A:270

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NW6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NW6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.LIP_BURCE125-134  1A:81-90

(-) Exons   (0, 0)

(no "Exon" information available for 2NW6)

(-) 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:320
 aligned with LIP_BURCE | P22088 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:320
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364
            LIP_BURCE    45 AAGYAATRYPIILVHGLSGTDKYAGVLEYWYGIQEDLQQNGATVYVANLSGFQSDDGPNGRGEQLLAYVKTVLAATGATKVNLVGHSQGGLSSRYVAAVAPDLVASVTTIGTPHRGSEFADFVQDVLAYDPTGLSSSVIAAFVNVFGILTSSSHNTNQDALAALQTLTTARAATYNQNYPSAGLGAPGSCQTGAPTETVGGNTHLLYSWAGTAIQPTLSVFGVTGATDTSTLPLVDPANVLDLSTLALFGTGTVMINRGSGQNDGLVSKCSALYGKVLSTSYKWNHLDEINQLLGVRGAYAEDPVAVIRTHANRLKLAGV 364
               SCOP domains d2nw6a_ A: automated matches                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2nw6A00 A:1-320  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains -----------------------------------------Abhydrolase_1-2nw6A01 A:42-236                                                                                                                                                                     ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeee.......eehhhee...hhhhhhhhh...eee.............hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh................eeee..eeeeeeeeee..eeeeeee..eeeeee........hhhhhhhhhhhhhhhhhhhhh..................eeeeeee....hhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------LIPASE_SER-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nw6 A   1 ADNYAATRYPIILVHGLTGTDKYAGVLEYWYGIQEDLQQRGATVYVANLSGFQSDDGPNGRGEQLLAYVKTVLAATGATKVNLVGHSQGGLTSRYVAAVAPDLVASVTTIGTPHRGSEFADFVQGVLAYDPTGLSSTVIAAFVNVFGILTSSSNNTNQDALAALKTLTTAQAATYNQNYPSAGLGAPGSCQTGAPTETVGGNTHLLYSWAGTAIQPTISVFGVTGATDTSTIPLVDPANALDPSTLALFGTGTVMVNRGSGQNDGVVSKCSALYGQVLSTSYKWNHLDEINQLLGVRGANAEDPVAVIRTHANRLKLAGV 320
                                    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       290       300       310       320
   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, 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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LIP_BURCE | P22088)
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: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.

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  2nw6
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  LIP_BURCE | P22088
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  3.1.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        LIP_BURCE | P22088: 1hqd 1oil 1ys1 1ys2 2lip 3lip 4lip 5lip

(-) Related Entries Specified in the PDB File

1hqd 1HQD AND THIS STRUCTURE ARE CRYSTAL STRUCTURES CONTAINING BOUND ENANTIOMERIC INHIBITORS
1oil 1OIL IS ISOMORPHOUS WITH THIS STRUCTURE
2lip 2LIP IS ISOMORPHOUS WITH THIS STRUCTURE
3lip 3LIP IS ISOMORPHOUS WITH THIS STRUCTURE
4lip 4LIP IS ISOMORPHOUS WITH THIS STRUCTURE
5lip 5LIP IS ISOMORPHOUS WITH THIS STRUCTURE