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(-) Description

Title :  RP2 LIPASE
 
Authors :  C. Withers-Martinez, C. Cambillau
Date :  13 Jul 96  (Deposition) - 12 Feb 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Esterase, Hydrolase, Lipid Degradation, Pancreas, Glycoprotein, Chimeric (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Withers-Martinez, F. Carriere, R. Verger, D. Bourgeois, C. Cambillau
A Pancreatic Lipase With A Phospholipase A1 Activity: Crystal Structure Of A Chimeric Pancreatic Lipase-Related Protein 2 From Guinea Pig.
Structure V. 4 1363 1996
PubMed-ID: 8939760  |  Reference-DOI: 10.1016/S0969-2126(96)00143-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RP2 LIPASE
    Cell Line: SF9
    Chains: A
    EC Number: 3.1.1.3
    Engineered: YES
    Expression System: SF9 CELLS
    Expression System Plasmid: PVL1393
    Expression System Strain: SF9
    Expression System Vector: BACULOVIRUS
    Mutation: YES
    Organ: PANCREATIC
    Organism Common: DOMESTIC GUINEA PIG
    Organism Scientific: CAVIA PORCELLUS
    Organism Taxid: 10141
    Synonym: RELATED PROTEIN 2 LIPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:187 , ARG A:190 , ASP A:192 , ASP A:195 , HOH A:519 , HOH A:520BINDING SITE FOR RESIDUE CA A 500
2CATUNKNOWNSER A:152 , ASP A:176 , HIS A:263CATALYTIC TRIAD. THE NUCLEOPHILE SER 152 IS LOCATED IN A BETA TURN AND HAS AN EPSILON CONFORMATION, COMMON FEATURE OF SERINE HYDROLASES.

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:10
2A:90 -A:101
3A:237 -A:261
4A:285 -A:296
5A:299 -A:304
6A:433 -A:449

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:15 -Pro A:16
2Leu A:210 -Pro A:211
3Phe A:297 -Pro A:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.LIPR2_CAVPO148-157  1A:146-155
LIPP_HUMAN163-172  1A:146-155
2PLATPS50095 PLAT domain profile.LIPR2_CAVPO322-434  1A:338-449
LIPP_HUMAN355-465  1A:338-449

(-) Exons   (0, 0)

(no "Exon" information available for 1GPL)

(-) 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:432
 aligned with LIPP_HUMAN | P16233 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:450
                                                                                   72                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                 71 |                                                                                                                                                                                                                                                                                                                                                                                                         
                                    26        36        46        56        66    | | 75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465
           LIPP_HUMAN    17 KEVCYERLGCFSDDSPWSGITERPLHILPWSPKDVNTRFLLYTNENPNNFQEVAA-DSSSISGSNFKTNRKTRFIIHGFIDKGEENWLANVCKNLFKVESVNCICVDWKGGSRTGYTQASQNIRIVGAEVAYFVEFLQSAFGYSPSNVHVIGHSLGAHAAGEAGRRTNGTIGRITGLDPAEPCFQGTPELVRLDPSDAKFVDVIHTDGAPIVPNLGFGMSQVVGHLDFFPNGGVEMPGCKKNILSQIVDIDGIWEGTRDFAACNHLRSYKYYTDSIVNPDGFAGFPCASYNVFTANKCFPCPSGGCPQMGHYADRYPGKTNDVGQKFYLDTGDASNFARWRYKVSVTLSGKKVTGHILVSLFGNKGNSKQYEIFKGTLKPDSTHSNEFDSDVDVGDLQMVKFIWYNNVINPTLPRVGASKIIVETNVGKQFNFCSPETVREEVLLTLTPC 465
               SCOP domains d1gpla2 A:1-336 Pancreatic lipase, N-terminal domain                                                                                                                                                                                                                                                                                              d1gpla1 A:337-449 Pancreatic lipase, C-terminal domain                                                           SCOP domains
               CATH domains 1gplA01 A:1-337  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                              1gplA02 A:338-448 Lipoxygenase-1                                                                              - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) .eeeehhheeee...................hhhh..eeeeee.......eee....hhhhhh.......eeeeee.........hhhhhhhhhhhhh..eeeeeee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhheeeeeehhhhhhhhhhhhh......eeeee.................hhh..eeeee......hhhh...........----hhhh........------------------...hhhhhhhhhhhhhh..hhhh.......hhhhh..................hhh.........eeeee..........eeeeeeeeeee..eeeeeeeeeee......eeeeeeeee....eeeeeeee......eeeeeeeeee.........eeeeeeeee.....eeeee..........eee... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeee---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLAT  PDB: A:338-449 UniProt: 355-465                                                                           PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gpl A   1 AEVCYSHLGCFSDEKPWAGTSQRPIKSLPSDPKKINTRFLLYTNENQNSYQLITATDIATIKASNFNLNRKTRFIIHGFTDSGENSWLSDMCKNMFQVEKVNCICVDWKGGSKAQYSQASQNIRVVGAEVAYLVQVLSTSLNYAPENVHIIGHSLGAHTAGEAGKRLNGLVGRITGLDPAEPYFQDTPEEVRLDPSDAKFVDVIHTDISPILPSLGFGMSQKVGHMDFFPNGGKDMPGCKT------------------GISCNHHRSIEYYHSSILNPEGFLGYPCASYDEFQESGCFPCPAKGCPKMGHFADQYPGKTNAVEQTFFLNTGASDNFTRWRYKVSVTLSGKKVTGHILVSLFGNKGNSKQYEIFKGTLKPDSTHSNEFDSDVDVGDLQMVKFIWYNNVINPTLPRVGASKIIVETNVGKQFNFCSPETVREEVLLTLTPC 449
                                    10        20        30|       39        49     |  58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238|        -       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398     ||409       419       429       439       449
                                                        30B                      54A                                                                                                                                                                                      239                258                                                                                                                                               404|                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                406                                           


Chain A from PDB  Type:PROTEIN  Length:432
 aligned with LIPR2_CAVPO | P81139 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:434
                                    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       330       340       350       360       370       380       390       400       410       420       430    
          LIPR2_CAVPO     1 AEVCYSHLGCFSDEKPWAGTSQRPIKSLPSDPKKINTRFLLYTNENQNSYQLITATDIATIKASNFNLNRKTRFIIHGFTDSGENSWLSDMCKNMFQVEKVNCICVDWKGGSKAQYSQASQNIRVVGAEVAYLVQVLSTSLNYAPENVHIIGHSLGAHTAGEAGKRLNGLVGRITGLDPAEPYFQDTPEEVRLDPSDAKFVDVIHTDISPILPSLGFGMSQKVGHMDFFPNGGKDMPGCKTGISCNHHRSIEYYHSSILNPEGFLGYPCASYDEFQESGCFPCPAKGCPKMGHFADQYPGKTNAVEQTFFLNTGASDNFTRWRYKVTVTLSGEKDPSGNINVALLGKNGNSAQYQVFKGTLKPDASYTNSIDVELNVGTIQKVTFLWKRSGISVSKPKMGASRITVQSGKDGTKYNFCSSDIVQENVEQTLSPC 434
               SCOP domains d1gpla2 A:1-336 Pancreatic lipase, N-terminal domain                                                                                                                                                                                                                                                                            d1gpla1 A:337- 449 Pancreatic lipase, C-terminal domain                                                            SCOP domains
               CATH domains 1gplA01 A:1-337  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                            1gplA02 A:338 -448 Lipoxygenase-1                                                                               - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeehhheeee...................hhhh..eeeeee.......eee....hhhhhh.......eeeeee.........hhhhhhhhhhhhh..eeeeeee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhheeeeeehhhhhhhhhhhhh......eeeee.................hhh..eeeee......hhhh...........----hhhh...........hhhhhhhhhhhhhh..hhhh.......hhhhh..................hhh.........eeeee..........eeeeeeeeeee..-eeeeeeeeeee......eeeeeeeee....eeeeeeee......eeeeeeeeee.........eeeeeeeee..-...eeeee..........eee... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER--------------------------------------------------------------------------------------------------------------------------------------------------------------------PLAT  PDB: A:338-449 UniProt: 322-434                                                                             PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpl A   1 AEVCYSHLGCFSDEKPWAGTSQRPIKSLPSDPKKINTRFLLYTNENQNSYQLITATDIATIKASNFNLNRKTRFIIHGFTDSGENSWLSDMCKNMFQVEKVNCICVDWKGGSKAQYSQASQNIRVVGAEVAYLVQVLSTSLNYAPENVHIIGHSLGAHTAGEAGKRLNGLVGRITGLDPAEPYFQDTPEEVRLDPSDAKFVDVIHTDISPILPSLGFGMSQKVGHMDFFPNGGKDMPGCKTGISCNHHRSIEYYHSSILNPEGFLGYPCASYDEFQESGCFPCPAKGCPKMGHFADQYPGKTNAVEQTFFLNTGASDNFTRWRYKVSVTLSGKK-VTGHILVSLFGNKGNSKQYEIFKGTLKPDSTHSNEFDSDVDVGDLQMVKFIWYNNVINPTLPRVGASKIIVETN-VGKQFNFCSPETVREEVLLTLTPC 449
                                    10        20        30|       39        49     |  58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238||     266       276       286       296       306       316       326       336       346   | | 355       365       375       385       395       406       416        |-|      435       445    
                                                        30B                      54A                                                                                                                                                                                      239|                                                                                         350 |                                                  404|                425 |                       
                                                                                                                                                                                                                                                                           258                                                                                           351                                                   406                  426
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LIPP_HUMAN | P16233)
molecular function
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    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:0030299    intestinal cholesterol absorption    Uptake of cholesterol into the blood by absorption from the small intestine.
    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:0044241    lipid digestion    The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested lipids into components that may be easily absorbed and directed into metabolism.
    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:0061365    positive regulation of triglyceride lipase activity    Any process that increases the activity of triglyceride lipase.
    GO:0001523    retinoid metabolic process    The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
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.

Chain A   (LIPR2_CAVPO | P81139)
molecular function
    GO:0047372    acylglycerol lipase activity    Catalysis of the reaction: H2O + acylglycerol = a fatty acid + glycerol.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    GO:0047714    galactolipase activity    Catalysis of the reaction: 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + 2 H2O = 3-beta-D-galactosyl-sn-glycerol + 2 carboxylates.
    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:0004620    phospholipase activity    Catalysis of the hydrolysis of a glycerophospholipid.
    GO:0004806    triglyceride lipase activity    Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate.
biological process
    GO:0019376    galactolipid catabolic process    The chemical reactions and pathways resulting in the breakdown of galactolipids, any glycolipid containing one of more residues of galactose and/or N-acetylgalactosamine.
    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.
    GO:0009395    phospholipid catabolic process    The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
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.
    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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 Related Entries

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

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        LIPP_HUMAN | P16233: 1lpa 1lpb 1n8s

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