Summary: Vacuolar protein sorting protein 36 Vps36
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Vacuolar protein sorting protein 36 Vps36 Provide feedback
Vps36 is a subunit of ESCRT-II, a protein involved in driving protein sorting from endosomes to lysosomes. The GLUE domain of Vps36 allows for a tight interaction to occur between the protein and Vps28, a subunit of ESCRT-I. This interaction is critical for ubiquitinated cargo progression from early to late endosomes [1].
Literature references
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Teo H, Gill DJ, Sun J, Perisic O, Veprintsev DB, Vallis Y, Emr SD, Williams RL; , Cell. 2006;125:99-111.: ESCRT-I core and ESCRT-II GLUE domain structures reveal role for GLUE in linking to ESCRT-I and membranes. PUBMED:16615893 EPMC:16615893
Internal database links
SCOOP: | GRAM Voldacs |
Similarity to PfamA using HHSearch: | GRAM PH_TFIIH bPH_3 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR021648
Vps36 is a subunit of ESCRT-II, a protein complex involved in driving protein sorting from endosomes to lysosomes. The GLUE domain of Vps36 allows for a tight interaction to occur between the protein and Vps28, a subunit of ESCRT-I. This interaction is critical for ubiquitinated cargo progression from early to late endosomes [PUBMED:16615893].
The multivesicular body (MVB) protein-sorting pathway targets transmembrane proteins either for degradation or for function in the vacuole/lysosomes. The signal for entry into this pathway is monoubiquitination of protein cargo, which results in incorporation of cargo into luminal vesicles at late endosomes. Another crucial player is phosphatidylinositol 3-phosphate (PtdINS(3)P), which is enriched on early endosomes and on the luminal vesicles of MVBs. The ESCRT complexes are critical for MVB budding and sorting of monoubiquitinated cargo into the luminal vesicles. Various Ub-binding domains (UBDs), such as UIM, UEV and NZF are found in such machineries. The Vps 36 subunit of the ESCRT-II trafficking complex binds both phosphoinositides and ubiquitin. All members of the Vps36 family contain a divergent GRAM/PH-like domain and yeast and some other fungi have one or two NZF domains inserted in the GRAM/PH-like domain.
The N-terminal region of Vps36 (EAP45) has been named the GLUE (GRAM-like ubiquitin-binding in EAP45) domain. The GLUE domain acts as a central cog driving the endosomal ESCRT machinery, through simultaneous interactions with PtdIns3P-containing membranes, ubiquitin, and ESCRT-I. Like other known ubiquitin-binding domains, the GLUE domain interacts with the hydrophobic surface patch of ubiquitin. The GLUE domain is the first ubiquitin-binding domain shown to bind phosphoinositides, and the ability of the same domain to bind both ubiquitin and a phosphoinositide opens interesting possibilities for coordination of membrane interactions and cargo recognition [PUBMED:15755741, PUBMED:16615893, PUBMED:17057714, PUBMED:16615903, PUBMED:17034365].
The GLUE domain has a split PH-domain fold with two curved beta sheets and one long alpha helix. The two sheets (beta1-beta4 and beta5- beta7) form a beta barrel-like structure, the C-terminal alpha helix is wedged between the two beta sheets, covering a hydrophobic core. The Vps36 GLUE domain binds PtdIns3P via a positively charged lipid binding pocket, delineated by the variable loops beta1/beta2, beta5/beta6 and beta7/alpha1, in contrast to the vast majority of characterised PH domains, which use a different lipid binding pocket [PUBMED:16615893, PUBMED:17057714].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | ubiquitin binding (GO:0043130) |
phosphatidylinositol-3-phosphate binding (GO:0032266) |
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 PH (CL0266), which has the following description:
Members of this clan share a PH-like fold. Many families in this clan bind to short peptide motifs in proteins and are involved in signalling.
The clan contains the following 73 members:
ASK_PH BBL5 bPH_1 bPH_2 bPH_3 bPH_4 bPH_5 bPH_6 CARM1 Carm_PH DCP1 DUF1126 DUF1681 DUF3203 EbsA FERM_C Glycoprot_B_PH1 Glycoprot_B_PH2 GRAM hSac2 ICAP-1_inte_bdg INPP5B_PH IQ_SEC7_PH IRS ISP1_C ISP3_C Jak1_Phl Mcp5_PH Myosin_TH1 OCRL_clath_bd PH PH_10 PH_11 PH_12 PH_13 PH_14 PH_15 PH_16 PH_17 PH_18 PH_19 PH_2 PH_3 PH_4 PH_5 PH_6 PH_8 PH_9 PH_BEACH PH_RBD PH_TFIIH PID PID_2 POB3_N Proteasom_Rpn13 PTB Ran_BP1 Rtt106 SCAB-PH Sec3-PIP2_bind Sharpin_PH SIN1_PH SNX17_FERM_C SPT16 SSrecog SYCP2_SLD UCH_N VID27_PH Voldacs Vps36_ESCRT-II WH1 YcxB ZFYVE21_CAlignments
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 (19) |
Full (1057) |
Representative proteomes | UniProt (1691) |
NCBI (2103) |
Meta (0) |
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RP15 (164) |
RP35 (465) |
RP55 (753) |
RP75 (1073) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (19) |
Full (1057) |
Representative proteomes | UniProt (1691) |
NCBI (2103) |
Meta (0) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (164) |
RP35 (465) |
RP55 (753) |
RP75 (1073) |
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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: | pdb_2cay |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Pollington J |
Number in seed: | 19 |
Number in full: | 1057 |
Average length of the domain: | 87.20 aa |
Average identity of full alignment: | 33 % |
Average coverage of the sequence by the domain: | 16.85 % |
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: | 92 | ||||||||||||
Family (HMM) version: | 9 | ||||||||||||
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 Vps36_ESCRT-II domain has been found. There are 4 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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