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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SEMET PATATIN
 
Authors :  T. J. Rydel, J. M. Williams, E. Krieger, F. Moshiri, W. C. Stallings, S. M. Brown, J. C. Pershing, J. P. Purcell, M. F. Alibhai
Date :  03 Apr 03  (Deposition) - 27 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Alpha/Beta Class Fold With Approximately Three Layers, Alpha/Beta/Alpha In Content. Possesses A Central Six- Stranded Beta Sheet With Alpha-Helices Front & Back, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Rydel, J. M. Williams, E. Krieger, F. Moshiri, W. C. Stallings, S. M. Brown, J. C. Pershing, J. P. Purcell, M. F. Alibhai
The Crystal Structure, Mutagenesis, And Activity Studies Reveal That Patatin Is A Lipid Acyl Hydrolase With A Ser-Asp Catalytic Dyad
Biochemistry V. 42 6696 2003
PubMed-ID: 12779324  |  Reference-DOI: 10.1021/BI027156R
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PATATIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Taxid: 562
    Expression System Variant: B834(DE3)
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: SOLANUM CARDIOPHYLLUM
    Organism Taxid: 160510

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 34)

Asymmetric/Biological Unit (1, 34)
No.NameCountTypeFull Name
1MSE34Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1OXW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNPLAPS51635 Patatin-like phospholipase (PNPLA) domain profile.PAT17_SOLCD32-229
 
 		  3A:32-229
B:1032-1229
C:2032-2229

(-) Exons   (0, 0)

(no "Exon" information available for 1OXW)

(-) 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:360
 aligned with PAT17_SOLCD | Q8LPW4 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:360
                                    34        44        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       374       384
         PAT17_SOLCD     25 LGEMVTVLSIDGGGIRGIIPATILEFLEGQLQEMDNNADARLADYFDVIGGTSTGGLLTAMISTPNENNRPFAAAKEIVPFYFEHGPQIFNPSGQILGPKYDGKYLMQVLQEKLGETRVHQALTEVVISSFDIKTNKPVIFTKSNLANSPELDAKMYDISYSTAAAPTYFPPHYFVTNTSNGDEYEFNLVDGAVATVADPALLSISVATRLAQKDPAFASIRSLNYKKMLLLSLGTGTTSEFDKTYTAKEAATWTAVHWMLVIQKMTDAASSYMTDYYLSTAFQALDSKNNYLRVQENALTGTTTEMDDASEANMELLVQVGENLLKKPVSEDNPETYEEALKRFAKLLSDRKKLRANKA  384
               SCOP domains d1oxwa_ A: Patatin                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1oxwA00 A:25-384 Cytosolic phospholipase A2 catalytic domain                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..hhhhh..eeeeeeee....eeeeee......hhhhh.hhhhhhhhhhh.......eeeeee.....eeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhhh.....hhh.eeeeee............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhh....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------PNPLA  PDB: A:32-229 UniProt: 32-229                                                                                                                                                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1oxw A   25 LGEmVTVLSIDGGGIRGIIPATILEFLEGQLQEmDNNADARLADYFDVIGGTSTGGLLTAmISTPNENNRPFAAAKEIVPFYFEHGPQIFNPSGQILGPKYDGKYLmQVLQEKLGETRVHQALTEVVISSFDIKTNKPVIFTKSNLANSPELDAKmYDISYSTAAAPTYFPPHYFVTNTSNGDEYEFNLVDGAVATVADPALLSISVATRLAQKDPAFASIRSLNYKKmLLLSLGTGTTSEFDKTYTAKEAATWTAVHWmLVIQKmTDAASSYmTDYYLSTAFQALDSKNNYLRVQENALTGTTTEmDDASEANmELLVQVGENLLKKPVSEDNPETYEEALKRFAKLLSDRKKLRANKA  384
                               |    34        44        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       374       384
                               |                            58-MSE                     85-MSE                                       131-MSE                                          180-MSE                                                                  253-MSE                        284-MSE |     298-MSE                          331-MSE 339-MSE                                         
                              28-MSE                                                                                                                                                                                                                                                               290-MSE                                                                                          


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with PAT17_SOLCD | Q8LPW4 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:359
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373         
         PAT17_SOLCD     24 QLGEMVTVLSIDGGGIRGIIPATILEFLEGQLQEMDNNADARLADYFDVIGGTSTGGLLTAMISTPNENNRPFAAAKEIVPFYFEHGPQIFNPSGQILGPKYDGKYLMQVLQEKLGETRVHQALTEVVISSFDIKTNKPVIFTKSNLANSPELDAKMYDISYSTAAAPTYFPPHYFVTNTSNGDEYEFNLVDGAVATVADPALLSISVATRLAQKDPAFASIRSLNYKKMLLLSLGTGTTSEFDKTYTAKEAATWTAVHWMLVIQKMTDAASSYMTDYYLSTAFQALDSKNNYLRVQENALTGTTTEMDDASEANMELLVQVGENLLKKPVSEDNPETYEEALKRFAKLLSDRKKLRAN  382
               SCOP domains d1oxwb_ B: Patatin                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1oxwB00 B:1024-1382 Cytosolic phospholipase A2 catalytic domain                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhheeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..hhhhh..eeeeeeee....eeeeee......hhhhh.hhhhhhhhhhh.......eeeeee.....eeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhhh.....hhh.eeeeee............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhh....hhhhhhhhhhhhhhhh..eee..eeeehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PNPLA  PDB: B:1032-1229 UniProt: 32-229                                                                                                                                                               --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1oxw B 1024 QLGEmVTVLSIDGGGIRGIIPATILEFLEGQLQEmDNNADARLADYFDVIGGTSTGGLLTAmISTPNENNRPFAAAKEIVPFYFEHGPQIFNPSGQILGPKYDGKYLmQVLQEKLGETRVHQALTEVVISSFDIKTNKPVIFTKSNLANSPELDAKmYDISYSTAAAPTYFPPHYFVTNTSNGDEYEFNLVDGAVATVADPALLSISVATRLAQKDPAFASIRSLNYKKmLLLSLGTGTTSEFDKTYTAKEAATWTAVHWmLVIQKmTDAASSYmTDYYLSTAFQALDSKNNYLRVQENALTGTTTEmDDASEANmELLVQVGENLLKKPVSEDNPETYEEALKRFAKLLSDRKKLRAN 1382
                                | 1033      1043      1053    | 1063      1073      1083 |    1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283|     1293    | 1303      1313      1323      1333     |1343      1353      1363      1373         
                             1028-MSE                      1058-MSE                   1085-MSE                                      1131-MSE                                         1180-MSE                                                                 1253-MSE                       1284-MSE |       |                             1331-MSE   |                                           
                                                                                                                                                                                                                                                                                                   1290-MSE   |                                     1339-MSE                                       
                                                                                                                                                                                                                                                                                                           1298-MSE                                                                                


Chain C from PDB  Type:PROTEIN  Length:362
 aligned with PAT17_SOLCD | Q8LPW4 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:362
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381  
         PAT17_SOLCD     22 FAQLGEMVTVLSIDGGGIRGIIPATILEFLEGQLQEMDNNADARLADYFDVIGGTSTGGLLTAMISTPNENNRPFAAAKEIVPFYFEHGPQIFNPSGQILGPKYDGKYLMQVLQEKLGETRVHQALTEVVISSFDIKTNKPVIFTKSNLANSPELDAKMYDISYSTAAAPTYFPPHYFVTNTSNGDEYEFNLVDGAVATVADPALLSISVATRLAQKDPAFASIRSLNYKKMLLLSLGTGTTSEFDKTYTAKEAATWTAVHWMLVIQKMTDAASSYMTDYYLSTAFQALDSKNNYLRVQENALTGTTTEMDDASEANMELLVQVGENLLKKPVSEDNPETYEEALKRFAKLLSDRKKLRANK  383
               SCOP domains d1oxwc_ C: Patatin                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -1oxwC00 C:2023-2383 Cytosolic phospholipase A2 catalytic domain                                                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ----------Patatin-1oxwC01 C:2032-2228                                                                                                                                                                          ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Patatin-1oxwC02 C:2032-2228                                                                                                                                                                          ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------Patatin-1oxwC03 C:2032-2228                                                                                                                                                                          ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .hhhhhheeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..hhhhh..eeeeeeee....eeeeee......hhhhh.hhhhhhhhhh........eeeeee.....eeeeeeee.hhhh...hhhhhhhhhhhhhhhhhhhh.....hhh.eeeeee............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhh....hhhhhhhhhhhhhhhhhheee..eeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------PNPLA  PDB: C:2032-2229 UniProt: 32-229                                                                                                                                                               ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1oxw C 2022 mAQLGEmVTVLSIDGGGIRGIIPATILEFLEGQLQEmDNNADARLADYFDVIGGTSTGGLLTAmISTPNENNRPFAAAKEIVPFYFEHGPQIFNPSGQILGPKYDGKYLmQVLQEKLGETRVHQALTEVVISSFDIKTNKPVIFTKSNLANSPELDAKmYDISYSTAAAPTYFPPHYFVTNTSNGDEYEFNLVDGAVATVADPALLSISVATRLAQKDPAFASIRSLNYKKmLLLSLGTGTTSEFDKTYTAKEAATWTAVHWmLVIQKmTDAASSYmTDYYLSTAFQALDSKNNYLRVQENALTGTTTEmDDASEANmELLVQVGENLLKKPVSEDNPETYEEALKRFAKLLSDRKKLRANK 2383
                            |     2031      2041      2051      2061      2071      2081   |  2091      2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211      2221      2231      2241      2251 |    2261      2271      2281  |   2291      2301      2311      2321      2331      2341      2351      2361      2371      2381  
                         2022-MSE |                          2058-MSE                   2085-MSE                                      2131-MSE                                         2180-MSE                                                                 2253-MSE                       2284-MSE |       |                             2331-MSE   |                                            
                               2028-MSE                                                                                                                                                                                                                                                              2290-MSE   |                                     2339-MSE                                        
                                                                                                                                                                                                                                                                                                             2298-MSE
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: Patatin (10)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (PAT17_SOLCD | Q8LPW4)
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:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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  1oxw
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAT17_SOLCD | Q8LPW4: 4pk9 4pka 4pkb

(-) Related Entries Specified in the PDB File

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