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19  structures 365  species 2  interactions 4026  sequences 76  architectures

Family: CRAL_TRIO (PF00650)

Summary: CRAL/TRIO domain

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This is the Wikipedia entry entitled "CRAL-TRIO domain". More...

CRAL-TRIO domain Edit Wikipedia article

CRAL/TRIO domain
1r5l opm.png
Alpha-tocopherol transfer protein, closed state with ligand.[1]
Identifiers
Symbol CRAL_TRIO
Pfam PF00650
InterPro IPR001251
SMART Sec14
SCOP 1aua
SUPERFAMILY 1aua
OPM superfamily 129
OPM protein 1r5l

CRAL-TRIO domain is a protein structural domain that binds small lipophilic molecules.[2] This domain is named after cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor.

CRALB protein carries 11-cis-retinol or 11-cis-retinaldehyde. It modulates interaction of retinoids with visual cycle enzymes. TRIO is involved in coordinating actin remodeling, which is necessary for cell migration and growth.

Other members of the family are alpha-tocopherol transfer protein and phosphatidylinositol-transfer protein (Sec14). They transport their substrates (alpha-tocopherol and phosphatidylinositol or phosphatidylcholine, respectively) between different intracellular membranes. Family also include a guanine nucleotide exchange factor that may function as an effector of RAC1 small G-protein.

The N-terminal domain of yeast ECM25 protein has been identified as containing a lipid binding CRAL-TRIO domain.[3]

Structure

The Sec14 protein was the first CRAL-TRIO domain for which the structure was determined.[4] The structure contains several alpha helices as well as a beta sheet composed of 6 strands. Strands 2,3,4 and 5 form a parallel beta sheet with strands 1 and 6 being anti-parallel. The structure also identified a hydrophobic binding pocket for lipid binding.

Human proteins containing this domain

C20orf121; MOSPD2; PTPN9; RLBP1; RLBP1L1; RLBP1L2; SEC14L1; SEC14L2; SEC14L3; SEC14L4; TTPA;


References

  1. ^ Min KC, Kovall RA, Hendrickson WA (December 2003). "Crystal structure of human alpha-tocopherol transfer protein bound to its ligand: implications for ataxia with vitamin E deficiency". Proc. Natl. Acad. Sci. U.S.A. 100 (25): 14713–8. doi:10.1073/pnas.2136684100. PMC 299775. PMID 14657365. 
  2. ^ Panagabko C, Morley S, Hernandez M, et al. (June 2003). "Ligand specificity in the CRAL-TRIO protein family". Biochemistry 42 (21): 6467–74. doi:10.1021/bi034086v. PMID 12767229. 
  3. ^ Gallego O, Betts MJ, Gvozdenovic-Jeremic J, et al. (November 2010). "A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae". Mol. Syst. Biol. 6 (1): 430. doi:10.1038/msb.2010.87. PMC 3010107. PMID 21119626. 
  4. ^ Sha B, Phillips SE, Bankaitis VA, Luo M (January 1998). "Crystal structure of the Saccharomyces cerevisiae phosphatidylinositol-transfer protein". Nature 391 (6666): 506–10. doi:10.1038/35179. PMID 9461221. 

External links

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CRAL/TRIO domain Provide feedback

No Pfam abstract.

Literature references

  1. Sha B, Phillips SE, Bankaitis VA, Luo M; , Nature 1998;391:506-510.: Crystal structure of the Saccharomyces cerevisiae phosphatidylinositol-transfer protein. PUBMED:9461221 EPMC:9461221


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001251

The CRAL-TRIO domain is a protein structural domain that binds small lipophilic molecules [PUBMED:12767229]. The domain is named after cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor.

The CRAL-TRIO domain is found in GTPase-activating proteins (GAPs), guanine nucleotide exchange factors (GEFs) and a family of hydrophobic ligand binding proteins, including the yeast SEC14 protein and mammalian retinaldehyde- and alpha-tocopherol-binding proteins. The domain may either constitute all of the protein or only part of it [PUBMED:2198263, PUBMED:8349655, PUBMED:9461221, PUBMED:10829015].

The structure of the domain in SEC14 proteins has been determined [PUBMED:9461221]. The structure contains several alpha helices as well as a beta sheet composed of 6 strands. Strands 2,3,4 and 5 form a parallel beta sheet with strands 1 and 6 being anti-parallel. The structure also identified a hydrophobic binding pocket for lipid binding.

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 CRAL_TRIO (CL0512), which has the following description:

This superfamily includes the CRAL-TRIO domain.

The clan contains the following 2 members:

CRAL_TRIO CRAL_TRIO_2

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
(110)
Full
(4026)
Representative proteomes NCBI
(4545)
Meta
(94)
RP15
(1013)
RP35
(1571)
RP55
(2350)
RP75
(2809)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(110)
Full
(4026)
Representative proteomes NCBI
(4545)
Meta
(94)
RP15
(1013)
RP35
(1571)
RP55
(2350)
RP75
(2809)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(110)
Full
(4026)
Representative proteomes NCBI
(4545)
Meta
(94)
RP15
(1013)
RP35
(1571)
RP55
(2350)
RP75
(2809)
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.

HMM logo

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.

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: Prosite
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 110
Number in full: 4026
Average length of the domain: 152.30 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 37.53 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 159
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

CRAL_TRIO CRAL_TRIO_N

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 CRAL_TRIO domain has been found. There are 19 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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