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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE-2 REVEALS THE BASIS FOR DIVERGENT SUBSTRATE SPECIFICITIES OF THE TWO LYSOSOMAL THIOESTERASES (PPT1 AND PPT2)
 
Authors :  G. Calero, P. Gupta, M. C. Nonato, S. Tandel, E. R. Biehl, S. L. Hofmann, J
Date :  02 Jun 03  (Deposition) - 02 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycoprotein, Lysosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Calero, P. Gupta, M. C. Nonato, S. Tandel, E. R. Biehl, S. L. Hofmann, J. Clardy
The Crystal Structure Of Palmitoyl Protein Thioesterase-2 (Ppt2) Reveals The Basis For Divergent Substrate Specificities Of The Two Lysosomal Thioesterases, Ppt1 And Ppt2.
J. Biol. Chem. V. 278 37957 2003
PubMed-ID: 12855696  |  Reference-DOI: 10.1074/JBC.M301225200

(-) Compounds

Molecule 1 - PALMITOYL-PROTEIN THIOESTERASE 2 PRECURSOR
    ChainsA
    EC Number3.1.2.22
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GenePPT2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPALMITOYL- PROTEIN HYDROLASE 2, PPT-2, G14

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:190 , ARG A:202 , PRO A:205BINDING SITE FOR RESIDUE NAG A 2285
2AC2SOFTWAREPRO A:168 , ASN A:190 , HIS A:204 , PRO A:205BINDING SITE FOR RESIDUE GOL A 1614
3AC3SOFTWAREASP A:72 , PHE A:74 , ASP A:75 , ARG A:77 , GLU A:78BINDING SITE FOR RESIDUE GOL A 1615
4AC4SOFTWARESER A:111 , GLN A:142 , THR A:146 , TYR A:148 , HOH A:2287BINDING SITE FOR RESIDUE GOL A 1616

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:109 -A:117
2A:165 -A:176
3A:276 -A:296

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:232 -Pro A:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.38dENST0000039552338dENSE00001677395chr6:32121354-3212141360PPT2_HUMAN-00--
1.39bENST0000039552339bENSE00001776007chr6:32121776-32122181406PPT2_HUMAN-00--
1.40cENST0000039552340cENSE00002176567chr6:32122364-32122554191PPT2_HUMAN1-61611A:35-6127
1.41bENST0000039552341bENSE00001603945chr6:32122807-32122960154PPT2_HUMAN62-113521A:62-11352
1.42bENST0000039552342bENSE00001601337chr6:32123465-3212356096PPT2_HUMAN113-145331A:113-14533
1.43ENST0000039552343ENSE00002176462chr6:32123648-32123755108PPT2_HUMAN145-181371A:145-18137
1.44dENST0000039552344dENSE00001760316chr6:32125414-3212549784PPT2_HUMAN181-209291A:181-20929
1.45bENST0000039552345bENSE00002165253chr6:32125617-3212570185PPT2_HUMAN209-237291A:209-23729
1.50dENST0000039552350dENSE00001599324chr6:32130345-3213039955PPT2_HUMAN237-255191A:237-25519
1.51cENST0000039552351cENSE00001606526chr6:32130584-32131455872PPT2_HUMAN256-302471A:256-30247

(-) 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:268
 aligned with PPT2_HUMAN | Q9UMR5 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:268
                                    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        
           PPT2_HUMAN    35 SYKPVIVVHGLFDSSYSFRHLLEYINETHPGTVVTVLDLFDGRESLRPLWEQVQGFREAVVPIMAKAPQGVHLICYSQGGLVCRALLSVMDDHNVDSFISLSSPQMGQYGDTDYLKWLFPTSMRSNLYRICYSPWGQEFSICNYWHDPHHDDLYLNASSFLALINGERDHPNATVWRKNFLRVGHLVLIGGPDDGVITPWQSSFFGFYDANETVLEMEEQLVYLRDSFGLKTLLARGAIVRCPMAGISHTAWHSNRTLYETCIEPWLS 302
               SCOP domains d1pjaa_ A: Palmitoyl protein thioesterase 2                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1pjaA00 A:35-302  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                       CATH domains
               Pfam domains Palm_thioest-1pjaA01 A:35-298                                                                                                                                                                                                                                           ---- Pfam domains
         Sec.struct. author ....eeee.....hhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh....eeeeeee..........hhhhhhhh...hhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhh.hhhhhh......hhhhhhhhhh...eeeeee........hhhhhhh.ee.....eehhhhhhhhhh...hhhhhhhh..eeeee...........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.40c  PDB: A:35-61   Exon 1.41b  PDB: A:62-113 UniProt: 62-113           -------------------------------Exon 1.43  PDB: A:145-181            ---------------------------Exon 1.45b  PDB: A:209-237   ------------------Exon 1.51c  PDB: A:256-302 UniProt: 256-302     Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------Exon 1.42b  PDB: A:113-145       -----------------------------------Exon 1.44d  PDB: A:181-209   ---------------------------Exon 1.50d         ----------------------------------------------- Transcript 1 (2)
                 1pja A  35 SYKPVIVVHGLFDSSYSFRHLLEYINETHPGTVVTVLDLFDGRESLRPLWEQVQGFREAVVPIMAKAPQGVHLICYSQGGLVCRALLSVMDDHNVDSFISLSSPQMGQYGDTDYLKWLFPTSMRSNLYRICYSPWGQEFSICNYWHDPHHDDLYLNASSFLALINGERDHPNATVWRKNFLRVGHLVLIGGPDDGVITPWQSSFFGFYDANETVLEMEEQLVYLRDSFGLKTLLARGAIVRCPMAGISHTAWHSNRTLYETCIEPWLS 302
                                    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        

   Legend:   → Mismatch (orange background)
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  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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPT2_HUMAN | Q9UMR5)
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:0098599    palmitoyl hydrolase activity    Catalysis of a hydrolase reaction that removes a palmitoyl moiety from some substrate.
    GO:0008474    palmitoyl-(protein) hydrolase activity    Catalysis of the reaction: palmitoyl-protein + H2O = palmitate + protein.
    GO:0016790    thiolester hydrolase activity    Catalysis of the reaction: RCO-SR' + H2O = RCOOH + HSR'. This reaction is the hydrolysis of a thiolester bond, an ester formed from a carboxylic acid and a thiol (i.e., RCO-SR'), such as that found in acetyl-coenzyme A.
biological process
    GO:0035338    long-chain fatty-acyl-CoA biosynthetic process    The chemical reactions and pathways resulting in the formation of a long-chain fatty-acyl-CoA any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more.
    GO:0098734    macromolecule depalmitoylation    The removal of palymitoyl groups from a macromolecule.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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1ei9 PALMITOYL PROTEIN THIOESTERASE-1 (PPT1) LYSOSOMAL THIOESTERASES