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(-) Description

Title :  CRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1
 
Authors :  J. J. Bellizzi Iii, J. Widom, C. Kemp, J. Y. Lu, A. K. Das, S. L. Hofmann, J
Date :  24 Feb 00  (Deposition) - 26 Apr 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Hydrolase, Glycoprotein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. J. Bellizzi 3Rd. , J. Widom, C. Kemp, J. Y. Lu, A. K. Das, S. L. Hofmann J. Clardy
The Crystal Structure Of Palmitoyl Protein Thioesterase 1 And The Molecular Basis Of Infantile Neuronal Ceroid Lipofuscinosis.
Proc. Natl. Acad. Sci. Usa V. 97 4573 2000
PubMed-ID: 10781062  |  Reference-DOI: 10.1073/PNAS.080508097
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PALMITOYL PROTEIN THIOESTERASE 1
    ChainsA
    EC Number3.1.2.22
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System CellSF21 CELLS
    Expression System Taxid10469
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913

 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
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:191 , ILE A:194 , ASN A:197 , HIS A:198BINDING SITE FOR RESIDUE NDG A 400
2AC2SOFTWAREASN A:212 , SER A:214 , TYR A:215BINDING SITE FOR RESIDUE NAG A 410
3AC3SOFTWARELEU A:231 , ASN A:232 , NAG A:421BINDING SITE FOR RESIDUE NDG A 420
4AC4SOFTWARENDG A:420BINDING SITE FOR RESIDUE NAG A 421

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:46
2A:96 -A:128
3A:152 -A:160

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:130 -Pro A:131
2Asp A:237 -Pro A:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PPT1_BOVIN_001 *I72FPPT1_BOVIN  ---  ---AI72F
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EI9)

(-) Exons   (0, 0)

(no "Exon" information available for 1EI9)

(-) 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:279
 aligned with PPT1_BOVIN | P45478 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:279
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297         
           PPT1_BOVIN    28 DPPAPLPLVIWHGMGDSCCNPLSMGAIKKMVEKKIPGIHVLSLEIGKTLREDVENSFFLNVNSQVTTVCQILAKDPKLQQGYNAMGFSQGGQFLRAVAQRCPSPPMVNLISVGGQHQGVFGLPRCPGESSHICDFIRKTLNAGAYNKAIQERLVQAEYWHDPIREDIYRNHSIFLADINQERGVNESYKKNLMALKKFVMVKFLNDTIVDPVDSEWFGFYRSGQAKETIPLQESTLYTQDRLGLKAMDKAGQLVFLALEGDHLQLSEEWFYAHIIPFLE 306
               SCOP domains d1ei9a_ A: Palmitoyl protein thioesterase 1                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ei9A00 A:28-306  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee............hhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh....eeeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.hhhhhh.....hhhhhhhhhh..eeeeeee.......hhhhhhh.ee.......eehhhhhhhhhh...hhhhhhhh..eeeeee.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ei9 A  28 DPPAPLPLVIWHGMGDSCCNPLSMGAIKKMVEKKIPGIHVLSLEIGKTLREDVENSFFLNVNSQVTTVCQILAKDPKLQQGYNAMGFSQGGQFLRAVAQRCPSPPMVNLISVGGQHQGVFGLPRCPGESSHICDFIRKTLNAGAYNKAIQERLVQAEYWHDPIREDIYRNHSIFLADINQERGVNESYKKNLMALKKFVMVKFLNDTIVDPVDSEWFGFYRSGQAKETIPLQESTLYTQDRLGLKAMDKAGQLVFLALEGDHLQLSEEWFYAHIIPFLE 306
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297         

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EI9)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPT1_BOVIN | P45478)
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:0016290    palmitoyl-CoA hydrolase activity    Catalysis of the reaction: palmitoyl-CoA + H2O = CoA + palmitate.
biological process
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0051186    cofactor metabolic process    The chemical reactions and pathways involving a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0051181    cofactor transport    The directed movement of a cofactor into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A cofactor is a substance that is required for the activity of an enzyme or other protein.
    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:0007042    lysosomal lumen acidification    Any process that reduces the pH of the lysosomal lumen, measured by the concentration of the hydrogen ion.
    GO:0031579    membrane raft organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of membrane rafts, small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0006907    pinocytosis    An endocytosis process that results in the uptake of liquid material by cells from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, called pinosomes, formed by invagination of the plasma membrane.
    GO:0048549    positive regulation of pinocytosis    Any process that activates, maintains or increases the rate of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes.
    GO:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0002084    protein depalmitoylation    The removal of palymitoyl groups from a lipoprotein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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: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.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPT1_BOVIN | P454781eh5 1exw

(-) Related Entries Specified in the PDB File

1eh5 PALMITOYL PROTEIN THIOESTERASE 1 COMPLEXED WITH PALMITATE