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91  structures 280  species 4  interactions 3359  sequences 189  architectures

Family: PLAT (PF01477)

Summary: PLAT/LH2 domain

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PLAT domain Edit Wikipedia article

PLAT/LH2 domain
PDB 1lpa EBI.jpg
Structure of the lipase-procolipase complex.[1]
Identifiers
Symbol PLAT
Pfam PF01477
InterPro IPR001024
SMART SM00308
PROSITE PDOC50095
SCOP 1lpa
SUPERFAMILY 1lpa
OPM superfamily 88
OPM protein 1zq4
CDD cd00113

In molecular biology the PLAT domain is protein domain that is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain[2] or LH2 (Lipoxygenase homology) domain.[3] The known structure of pancreatic lipase shows this domain binds to procolipase Pfam PF01114, which mediates membrane association.

This domain is found in a variety of membrane or lipid associated proteins. It forms a beta-sandwich composed of two sheets of four strands each.[2][4][5]

Human proteins containing this domain[edit]

ALOX12; ALOX12B; ALOX12P2; ALOX15; ALOX15B; ALOX5; ALOXE3; LIPC; LIPG; LOXHD1; LPL; PKD1; PKD1L1; PKD1L2; PKD1L3; PKDREJ; PNLIP; PNLIPRP1; PNLIPRP2; PNLIPRP3; RAB6IP1;

References[edit]

  1. ^ van Tilbeurgh H, Egloff MP, Martinez C, Rugani N, Verger R, Cambillau C (April 1993). "Interfacial activation of the lipase-procolipase complex by mixed micelles revealed by X-ray crystallography". Nature 362 (6423): 814–20. doi:10.1038/362814a0. PMID 8479519. 
  2. ^ a b Bateman A, Sandford R (1999). "The PLAT domain: a new piece in the PKD1 puzzle". Curr. Biol. 9 (16): R588–90. doi:10.1016/S0960-9822(99)80380-7. PMID 10469604. 
  3. ^ Ponting CP, Hofmann K, Bork P (August 1999). "A latrophilin/CL-1-like GPS domain in polycystin-1". Curr. Biol. 9 (16): R585–8. doi:10.1016/S0960-9822(99)80379-0. PMID 10469603. 
  4. ^ Delrieu I, Waller CC, Mota MM, Grainger M, Langhorne J, Holder AA (2002). "PSLAP, a protein with multiple adhesive motifs, is expressed in Plasmodium falciparum gametocytes". Mol. Biochem. Parasitol. 121 (1): 11–20. doi:10.1016/S0166-6851(02)00016-6. PMID 11985859. 
  5. ^ Minor W, Tomchick DR, Phan P, Cymborowski M, Holman TR (2001). "Structural and functional characterization of second-coordination sphere mutants of soybean lipoxygenase-1". Biochemistry 40 (25): 7509–7517. doi:10.1021/bi002893d. PMID 11412104. 

This article incorporates text from the public domain Pfam and InterPro IPR001024

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

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

PLAT/LH2 domain Provide feedback

This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain binds to procolipase PF01114 which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners. The structure of this domain is known for many members of the family and is composed of a beta sandwich.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001024

Lipoxygenases (EC) are a class of iron-containing dioxygenases which catalyses the hydroperoxidation of lipids, containing a cis,cis-1,4-pentadiene structure. They are common in plants where they may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. In mammals a number of lipoxygenases isozymes are involved in the metabolism of prostaglandins and leukotrienes [PUBMED:3017195]. Sequence data is available for the following lipoxygenases:

  • Plant lipoxygenases (EC, INTERPRO). Plants express a variety of cytosolic isozymes as well as what seems to be a chloroplast isozyme [PUBMED:7508918].
  • Mammalian arachidonate 5-lipoxygenase (EC, INTERPRO).
  • Mammalian arachidonate 12-lipoxygenase (EC, INTERPRO).
  • Mammalian erythroid cell-specific 15-lipoxygenase (EC, INTERPRO).

The iron atom in lipoxygenases is bound by four ligands, three of which are histidine residues [PUBMED:8502991]. Six histidines are conserved in all lipoxygenase sequences, five of them are found clustered in a stretch of 40 amino acids. This region contains two of the three iron-ligands; the other histidines have been shown [PUBMED:1567851] to be important for the activity of lipoxygenases.

This entry represents a domain found in lipoxygenases and other enzymes. It is known as the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain, is found in a variety of membrane or lipid associated proteins. Structurally, this domain forms a beta-sandwich composed of two sheets of four strands each [PUBMED:10469604, PUBMED:11985859, PUBMED:11412104]. The most highly conserved regions coincide with the beta-strands, with most of the highly conserved residues being buried within the protein. An exception to this is a surface lysine or arginine that occurs on the surface of the fifth beta-strand of the eukaryotic domains. In pancreatic lipase, the lysine in this position forms a salt bridge with the procolipase protein. The conservation of a charged surface residue may indicate the location of a conserved ligand-binding site. It is thought that this domain may mediate membrane attachment via other protein binding partners.

Gene Ontology

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

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PLAT (CL0321), which has the following description:

This domain has an 8-stranded sandwich structure.

The clan contains the following 2 members:

ATS3 PLAT

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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.

  Seed
(84)
Full
(3359)
Representative proteomes NCBI
(3171)
Meta
(14)
RP15
(578)
RP35
(838)
RP55
(1202)
RP75
(1790)
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Format an alignment

  Seed
(84)
Full
(3359)
Representative proteomes NCBI
(3171)
Meta
(14)
RP15
(578)
RP35
(838)
RP55
(1202)
RP75
(1790)
Alignment:
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Order:
Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(84)
Full
(3359)
Representative proteomes NCBI
(3171)
Meta
(14)
RP15
(578)
RP35
(838)
RP55
(1202)
RP75
(1790)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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.

Pfam alignments:

HMM logo

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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.

Note: You can also download the data file for the tree.

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: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 84
Number in full: 3359
Average length of the domain: 109.70 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 17.37 %

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 20.8 20.8
Trusted cut-off 20.8 21.0
Noise cut-off 20.7 20.7
Model length: 113
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 4 interactions for this family. More...

Colipase Lipoxygenase Colipase_C Lipase

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 PLAT domain has been found. There are 91 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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