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6  structures 252  species 0  interactions 572  sequences 11  architectures

Family: Palm_thioest (PF02089)

Summary: Palmitoyl protein thioesterase

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This is the Wikipedia entry entitled "Palmitoyl protein thioesterase". More...

Palmitoyl protein thioesterase Edit Wikipedia article

Palmitoyl protein thioesterase
1eh5 opm.gif
Palmitoyl protein thioesterase 1. Red plane shows hydrocarbon boundary of the lipid bilayer
Identifiers
Symbol Palm_thioest
Pfam PF02089
Pfam clan CL0028
InterPro IPR002472
SCOP 1exw
SUPERFAMILY 1exw
OPM superfamily 135
OPM protein 1eh5
palmitoyl [protein] hydrolase
Identifiers
EC number 3.1.2.22
CAS number 150605-49-5
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO

Palmitoyl protein thioesterases are enzymes (EC 3.1.2.22) that remove thioester-linked fatty acyl groups such as palmitate from modified cysteine residues in proteins or peptides during lysosomal degradation.

Neuronal ceroid lipofuscinoses (NCL) represent a group of encephalopathies that occur in 1 in 12,500 children. Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis.[1] The most common mutation results in intracellular accumulation of the polypeptide and undetectable enzyme activity in the brain. Direct sequencing of cDNAs derived from brain RNA of INCL patients has shown a mis-sense transversion of A to T at nucleotide position 364, which results in substitution of Trp for Arg at position 122 in the protein - Arg 122 is immediately adjacent to a lipase consensus sequence that contains the putative active site Ser of PPT. The occurrence of this and two other independent mutations in the PPT gene strongly suggests that defects in this gene cause INCL.

Examples[edit]

Human proteins containing this domain include:

palmitoyl-protein thioesterase 1
Identifiers
Symbol PPT1
Alt. symbols PPT
Entrez 5538
HUGO 9325
OMIM 600722
RefSeq NM_000310
UniProt P50897
Other data
Locus Chr. 1 p32
palmitoyl-protein thioesterase 2
Identifiers
Symbol PPT2
Alt. symbols G14
Entrez 9374
HUGO 9326
OMIM 603298
RefSeq NM_138717
UniProt Q9UMR5
Other data
Locus Chr. 6 p21.3

See also[edit]

References[edit]

  1. ^ Hofmann SL, Vesa J, Hellsten E, Verkruyse LA, Camp LA, Rapola J, Santavuori P, Peltonen L (1995). "Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis". Nature 376 (6541): 584–587. doi:10.1038/376584a0. PMID 7637805. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR002472


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002472

Neuronal ceroid lipofuscinoses (NCL) represent a group of encephalopathies that occur in 1 in 12,500 children. Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis [PUBMED:7637805]. The most common mutation results in intracellular accumulation of the polypeptide and undetectable enzyme activity in the brain. Direct sequencing of cDNAs derived from brain RNA of INCL patients has shown a mis-sense transversion of A to T at nucleotide position 364, which results in substitution of Trp for Arg at position 122 in the protein - Arg 122 is immediately adjacent to a lipase consensus sequence that contains the putative active site Ser of PPT. The occurrence of this and two other independent mutations in the PPT gene strongly suggests that defects in this gene cause INCL.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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(2)
Full
(572)
Representative proteomes NCBI
(538)
Meta
(22)
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(127)
RP35
(185)
RP55
(265)
RP75
(338)
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  Seed
(2)
Full
(572)
Representative proteomes NCBI
(538)
Meta
(22)
RP15
(127)
RP35
(185)
RP55
(265)
RP75
(338)
Alignment:
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  Seed
(2)
Full
(572)
Representative proteomes NCBI
(538)
Meta
(22)
RP15
(127)
RP35
(185)
RP55
(265)
RP75
(338)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: IPR002472
Previous IDs: none
Type: Domain
Author: Mian N, Bateman A
Number in seed: 2
Number in full: 572
Average length of the domain: 229.00 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 83.50 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.2 21.2
Noise cut-off 21.0 21.0
Model length: 279
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Palm_thioest domain has been found. There are 6 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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