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(-) Description

Title :  BACILLUS SUBTILIS LIPASE A WITH COVALENTLY BOUND RC-IPG-PHOSPHONATE-INHIBITOR
 
Authors :  M. J. Droege, G. Van Pouderoyen, T. E. Vrenken, C. J. Rueggeberg, M. T. Reetz, B. W. Dijkstra, W. J. Quax
Date :  09 Oct 03  (Deposition) - 19 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lipase, Alpha/Beta Hydrolase, Phosphonate Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Droege, Y. L. Boersma, G. Van Pouderoyen, T. E. Vrenken, C. J. Rueggeberg, M. T. Reetz, B. W. Dijkstra, W. J. Quax
Directed Evolution Of Bacillus Subtilis Lipase A By Use Of Enantiomeric Phosphonate Inhibitors: Crystal Structures And Phage Display Selection
Chembiochem V. 7 149 2005
PubMed-ID: 16342303  |  Reference-DOI: 10.1002/CBIC.200500308
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIPASE
    Chains: A, B
    EC Number: 3.1.1.3
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PMA5LIP
    Expression System Strain: BCL1051
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-181
    Gene: LIPA
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: LIPASE A

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1RIL2Ligand/Ion[(4R)-2,2-DIMETHYL-1,3-DIOXOLAN-4-YL]METHYL HYDROGENHEX-5-ENYLPHOSPHONATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1RIL1Ligand/Ion[(4R)-2,2-DIMETHYL-1,3-DIOXOLAN-4-YL]METHYL HYDROGENHEX-5-ENYLPHOSPHONATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1RIL1Ligand/Ion[(4R)-2,2-DIMETHYL-1,3-DIOXOLAN-4-YL]METHYL HYDROGENHEX-5-ENYLPHOSPHONATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , ILE A:12 , GLY A:14 , HIS A:76 , SER A:77 , MET A:78 , HIS A:156BINDING SITE FOR RESIDUE RIL A 277
2AC2SOFTWAREGLY B:11 , ILE B:12 , HIS B:76 , SER B:77 , MET B:78 , HIS B:156BINDING SITE FOR RESIDUE RIL B 277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R4Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R4Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R4Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1R4Z)

(-) 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:179
 aligned with ESTA_BACSU | P37957 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:179
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203         
           ESTA_BACSU    34 HNPVVMVHGIGGASFNFAGIKSYLVSQGWSRDKLYAVDFWDKTGTNYNNGPVLSRFVQKVLDETGAKKVDIVAHSMGGANTLYYIKNLDGGNKVANVVTLGGANRLTTGKALPGTDPNQKILYTSIYSSADMIVMNYLSRLDGARNVQIHGVGHIGLLYSSQVNSLIKEGLNGGGQNTN 212
               SCOP domains d1r4za_ A: Lipase A                                                                                                                                                                 SCOP domains
               CATH domains 1r4zA00 A:3-181  [code=3.40.50.1820, no name defined]                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhhh..hhh.eee........hhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh.hhhh.eeeeeee..hhhhh..............eeeeeee......hhhhhh....eeeee....hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r4z A   3 HNPVVMVHGIGGASFNFAGIKSYLVSQGWSRDKLYAVDFWDKTGTNYNNGPVLSRFVQKVLDETGAKKVDIVAHSMGGANTLYYIKNLDGGNKVANVVTLGGANRLTTGKALPGTDPNQKILYTSIYSSADMIVMNYLSRLDGARNVQIHGVGHIGLLYSSQVNSLIKEGLNGGGQNTN 181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172         


Chain B from PDB  Type:PROTEIN  Length:179
 aligned with ESTA_BACSU | P37957 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:179
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203         
           ESTA_BACSU    34 HNPVVMVHGIGGASFNFAGIKSYLVSQGWSRDKLYAVDFWDKTGTNYNNGPVLSRFVQKVLDETGAKKVDIVAHSMGGANTLYYIKNLDGGNKVANVVTLGGANRLTTGKALPGTDPNQKILYTSIYSSADMIVMNYLSRLDGARNVQIHGVGHIGLLYSSQVNSLIKEGLNGGGQNTN 212
               SCOP domains d1r4zb_ B: Lipase A                                                                                                                                                                 SCOP domains
               CATH domains 1r4zB00 B:3-181  [code=3.40.50.1820, no name defined]                                                                                                                               CATH domains
           Pfam domains (1) Lipase_2-1r4zB01 B:3-110                                                                                    ----------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Lipase_2-1r4zB02 B:3-110                                                                                    ----------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhhh..hhh.eee........hhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh.eeeeeee..hhhhh..............eeeeeee......hhhhhh....eeeee....hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r4z B   3 HNPVVMVHGIGGASFNFAGIKSYLVSQGWSRDKLYAVDFWDKTGTNYNNGPVLSRFVQKVLDETGAKKVDIVAHSMGGANTLYYIKNLDGGNKVANVVTLGGANRLTTGKALPGTDPNQKILYTSIYSSADMIVMNYLSRLDGARNVQIHGVGHIGLLYSSQVNSLIKEGLNGGGQNTN 181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ESTA_BACSU | P37957)
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: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: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.

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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
        ESTA_BACSU | P37957: 1i6w 1isp 1r50 1t2n 1t4m 2qxt 2qxu 3d2a 3d2b 3d2c 3qmm 3qzu 5cri 5ct4 5ct5 5ct6 5ct8 5ct9 5cta 5cur

(-) Related Entries Specified in the PDB File

1i6w BACILLUS SUBTILIS LIPASE A
1r50 BACILLUS SUBTILIS LIPASE A WITH COVALENTLY BOUND SC-IPG- PHOSPHONATE-INHIBITOR