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CATH domain | Related DB codes (homologues) |
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3.40.50.1820 : Rossmann fold | S00544,S00344,S00517,S00525,S00526,S00720,S00723,S00724,S00725,S00919,S00057,S00374,S00345,S00347,S00348,S00346,S00352,S00353,S00355,S00356,S00358,D00189,D00210,D00539,T00253 |
KEGG pathways | MAP code | Pathways |
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MAP00062 | Fatty acid elongation in mitochondria |
UniProtKB:Accession Number | P45478 | O75608 |
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Entry name | PPT1_BOVIN | LYPA1_HUMAN |
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Activity | Palmitoyl-protein + H(2)O = palmitate + protein. | Palmitoyl-protein + H(2)O = palmitate + protein. |
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Subunit |
| Homodimer. |
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Subcellular location | Lysosome. | Cytoplasm (By similarity). |
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Cofactor |
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Compound table: links to PDB-related databases & PoSSuM |
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| Substrates | Products | intermediates |
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KEGG-id | C06412 | C00001 | C00249 | C00017 | I00147 | I00085 | I00086 |
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Compound | Palmitoyl-protein | H2O | Palmitate | Protein | Peptidyl-Ser-tetrahedral intermediate (with previous thioester) | Acyl-enzyme(Peptidyl-Ser-acyl group) | Peptidyl-Ser-tetrahedral-intermediate |
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Type | lipid,peptide/protein | H2O | fatty acid | peptide/protein |
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ChEBI |
| 15377
| 15756
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PubChem |
| 962 22247451
| 985
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| | | | | | | | | | | | | | |
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1eh5A |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound | Unbound | Intermediate-bound:PLM | Unbound |
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1ei9A |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1exwA |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:HDS |
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1fj2A |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1fj2B |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[2] | p.4575-4578 |
| [3] | p.23849-23851 |
| [4] | p.1142-1143 |
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references | [1] |
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PubMed ID | 10551886 |
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Journal | J Biol Chem |
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Year | 1999 |
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Volume | 274 |
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Pages | 33148-54 |
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Authors | Yeh DC, Duncan JA, Yamashita S, Michel T |
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Title | Depalmitoylation of endothelial nitric-oxide synthase by acyl-protein thioesterase 1 is potentiated by Ca(2+)-calmodulin. |
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[2] |
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Comments | X-ray crystallography (2.25 Angstroms) |
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PubMed ID | 10781062 |
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Journal | Proc Natl Acad Sci U S A |
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Year | 2000 |
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Volume | 97 |
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Pages | 4573-8 |
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Authors | Bellizzi JJ 3rd, Widom J, Kemp C, Lu JY, Das AK, Hofmann SL, Clardy J |
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Title | The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis. |
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Related PDB | 1eh5,1ei9 |
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[3] |
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Comments | X-ray crystallography (2.4 Angstroms), catalysis |
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PubMed ID | 10801859 |
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Journal | J Biol Chem |
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Year | 2000 |
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Volume | 275 |
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Pages | 23847-51 |
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Authors | Das AK, Bellizzi JJ 3rd, Tandel S, Biehl E, Clardy J, Hofmann SL |
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Title | Structural basis for the insensitivity of a serine enzyme (palmitoyl-protein thioesterase) to phenylmethylsulfonyl fluoride. |
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Related PDB | 1exw |
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[4] |
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Comments | X-ray crystallography (1.5 Angstroms) |
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PubMed ID | 11080636 |
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Journal | Structure Fold Des |
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Year | 2000 |
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Volume | 8 |
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Pages | 1137-46 |
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Authors | Devedjiev Y, Dauter Z, Kuznetsov SR, Jones TL, Derewenda ZS |
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Title | Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A. |
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Related PDB | 1fj2 |
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[5] |
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PubMed ID | 12693927 |
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Journal | Biochemistry |
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Year | 2003 |
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Volume | 42 |
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Pages | 4311-20 |
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Authors | Linder ME, Deschenes RJ |
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Title | New insights into the mechanisms of protein palmitoylation. |
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[6] |
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PubMed ID | 12909364 |
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Journal | Gene |
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Year | 2003 |
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Volume | 312 |
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Pages | 271-9 |
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Authors | Glaser RL, Hickey AJ, Chotkowski HL, Chu-LaGraff Q |
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Title | Characterization of Drosophila palmitoyl-protein thioesterase 1. |
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comments | This enzyme belongs to the palmitoyl-protein thioesterase family. According to the literature [4], these serine-dependent hydrolases catalyze a two-step reaction, acylation and deacylation, each proceeding through a tetrahedral transition state. In the initial stage, the interaction of the pair of the residues, Asp169-His203 (PDB; 1fj2), activates the nucleophilic serine residue. In the acyl-enzyme, the acylated serine moves from the catalytic His, giving room for a water, which makes a nucleophilic attack on the ester bond of the serine during the deacylation. During the acylation and deacylation, the tetrahedral transient oxyanions are stabilized in a positively charged oxyanion hole, formed by the mainchain amides of Leu25 and Gln115 (PDB; 1fj2) (see [4]).
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created | updated |
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2002-07-04 | 2012-10-05 |
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