Summary: CRAL/TRIO domain
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CRAL-TRIO domain Edit Wikipedia article
CRAL/TRIO domain | |||||||||
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![]() Alpha-tocopherol transfer protein, closed state with ligand.[1] | |||||||||
Identifiers | |||||||||
Symbol | CRAL_TRIO | ||||||||
Pfam | PF00650 | ||||||||
InterPro | IPR001251 | ||||||||
SMART | Sec14 | ||||||||
SCOPe | 1aua / SUPFAM | ||||||||
OPM superfamily | 121 | ||||||||
OPM protein | 1r5l | ||||||||
CDD | cd00170 | ||||||||
Membranome | 576 | ||||||||
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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
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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
- UMich Orientation of Proteins in Membranes families/superfamily-129 - Calculated spatial positions of CRAL-TRIO domains in membrane
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CRAL/TRIO domain Provide feedback
No Pfam abstract.
Literature references
-
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
SCOOP: | CRAL_TRIO_2 CRAL_TRIO_N |
Similarity to PfamA using HHSearch: | CRAL_TRIO_2 |
External database links
PROSITE profile: | PS50191 |
SCOP: | 1aua |
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_2Alignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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 (102) |
Full (17582) |
Representative proteomes | UniProt (28948) |
NCBI (43621) |
Meta (88) |
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RP15 (3284) |
RP35 (8430) |
RP55 (13174) |
RP75 (17682) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (102) |
Full (17582) |
Representative proteomes | UniProt (28948) |
NCBI (43621) |
Meta (88) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (3284) |
RP35 (8430) |
RP55 (13174) |
RP75 (17682) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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
Seed source: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 102 |
Number in full: | 17582 |
Average length of the domain: | 152.90 aa |
Average identity of full alignment: | 20 % |
Average coverage of the sequence by the domain: | 34.71 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 159 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 47 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 sequence.
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