Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
24  structures 1416  species 0  interactions 7043  sequences 156  architectures

Family: LisH (PF08513)

Summary: LisH

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "LisH domain". More...

LisH domain Edit Wikipedia article

LisH
PDB 1uuj EBI.jpg
n-terminal domain of lissencephaly-1 protein (lis-1)
Identifiers
Symbol LisH
Pfam PF08513
InterPro IPR013720

In molecular biology, the LisH domain (lis homology domain) is a protein domain found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerisation motif, and that other structural elements are likely to play an important role in dimerisation.[1][2][3]

The LisH domain is found in the Saccharomyces cerevisiae SIF2 protein, a component of the SET3 complex which is responsible for repressing meiotic genes In SIF2 the LisH domain has been shown to mediate dimer and tetramer formation.[4] It has been shown that the LisH domain helps mediate interaction with components of the SET3 complex.[4]

References

  1. ^ Kim MH, Cooper DR, Oleksy A, Devedjiev Y, Derewenda U, Reiner O, Otlewski J, Derewenda ZS (June 2004). "The structure of the N-terminal domain of the product of the lissencephaly gene Lis1 and its functional implications". Structure. 12 (6): 987–98. PMID 15274919. doi:10.1016/j.str.2004.03.024. 
  2. ^ Mateja A, Cierpicki T, Paduch M, Derewenda ZS, Otlewski J (March 2006). "The dimerization mechanism of LIS1 and its implication for proteins containing the LisH motif". J. Mol. Biol. 357 (2): 621–31. PMID 16445939. doi:10.1016/j.jmb.2006.01.002. 
  3. ^ Gerlitz G, Darhin E, Giorgio G, Franco B, Reiner O (November 2005). "Novel functional features of the Lis-H domain: role in protein dimerization, half-life and cellular localization". Cell Cycle. 4 (11): 1632–40. PMID 16258276. doi:10.4161/cc.4.11.2151. 
  4. ^ a b Cerna D, Wilson DK (2005). "The structure of Sif2p, a WD repeat protein functioning in the SET3 corepressor complex.". J Mol Biol. 351 (4): 923–35. PMID 16051270. doi:10.1016/j.jmb.2005.06.025. 

This article incorporates text from the public domain Pfam and InterPro IPR013720

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.

LisH Provide feedback

The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex [1].

Literature references

  1. Cerna D, Wilson DK; , J Mol Biol 2005;351:923-935.: The structure of Sif2p, a WD repeat protein functioning in the SET3 corepressor complex. PUBMED:16051270 EPMC:16051270


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006594

The 33-residue LIS1 homology (LisH) motif is found in eukaryotic intracellular proteins involved in microtubule dynamics, cell migration, nucleokinesis and chromosome segregation. The LisH motif is likely to possess a conserved protein-binding function and it has been proposed that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly. The LisH motif is found associated to other domains, such as WD-40, SPRY, Kelch, AAA ATPase, RasGEF, or HEAT [ PUBMED:11734546 , PUBMED:12384287 , PUBMED:12559565 , PUBMED:16051270 ].

The secondary structure of the LisH domain is predicted to be two alpha- helices [ PUBMED:11734546 ].

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan LisH (CL0561), which has the following description:

Members of this clan include the LisH dimerisation/tetramerisation domains and the FOP N terminal dimerisation domain.

The clan contains the following 4 members:

FOP_dimer LisH LisH_2 LisH_TPL

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

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
(50)
Full
(7043)
Representative proteomes UniProt
(11566)
RP15
(1063)
RP35
(3055)
RP55
(5506)
RP75
(7546)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(50)
Full
(7043)
Representative proteomes UniProt
(11566)
RP15
(1063)
RP35
(3055)
RP55
(5506)
RP75
(7546)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(50)
Full
(7043)
Representative proteomes UniProt
(11566)
RP15
(1063)
RP35
(3055)
RP55
(5506)
RP75
(7546)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Pfam-B_8344 (release 17.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Wood V
Number in seed: 50
Number in full: 7043
Average length of the domain: 26.50 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 4.79 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 27
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 LisH domain has been found. There are 24 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.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0V520 View 3D Structure Click here
A0A0R0FPP1 View 3D Structure Click here
A0A0R0JDA7 View 3D Structure Click here
A0A0R0JUX7 View 3D Structure Click here
A0A0R0K565 View 3D Structure Click here
A0A1D6EF10 View 3D Structure Click here
A0A1D6FF36 View 3D Structure Click here
A0A1D6FYR6 View 3D Structure Click here
A0A1D6HP54 View 3D Structure Click here
A0A1D6J4G2 View 3D Structure Click here
A0A1D6JVD0 View 3D Structure Click here
A0A1D6LCJ6 View 3D Structure Click here
A0A1D6NLM5 View 3D Structure Click here
A0A1D6NLR6 View 3D Structure Click here
A0A1D8PSS1 View 3D Structure Click here
A0A1P8B5A1 View 3D Structure Click here
A0A2R9YJJ0 View 3D Structure Click here
A0A368UGQ3 View 3D Structure Click here
A1L252 View 3D Structure Click here
A2RUX0 View 3D Structure Click here
A5WVU0 View 3D Structure Click here
B4FSH1 View 3D Structure Click here
B4G110 View 3D Structure Click here
D3Z7Z5 View 3D Structure Click here
D3ZNF4 View 3D Structure Click here
E7FGY2 View 3D Structure Click here
F1LVV3 View 3D Structure Click here
F1M5A4 View 3D Structure Click here
F1QSI7 View 3D Structure Click here
F4I7D4 View 3D Structure Click here
G3V6G5 View 3D Structure Click here
H2L2B2 View 3D Structure Click here
I1K293 View 3D Structure Click here
I1LA80 View 3D Structure Click here
I1M296 View 3D Structure Click here
I1M9M2 View 3D Structure Click here
I1MED3 View 3D Structure Click here
I1MUE4 View 3D Structure Click here
K7K8T5 View 3D Structure Click here
K7KI15 View 3D Structure Click here
K7KXZ7 View 3D Structure Click here
K7LAS2 View 3D Structure Click here
K7LN56 View 3D Structure Click here
K7MA64 View 3D Structure Click here
K7MSV4 View 3D Structure Click here
O13282 View 3D Structure Click here
O48847 View 3D Structure Click here
O60907 View 3D Structure Click here
O74522 View 3D Structure Click here
O74845 View 3D Structure Click here
O94619 View 3D Structure Click here
O94712 View 3D Structure Click here
P38129 View 3D Structure Click here
P38262 View 3D Structure Click here
P43034 View 3D Structure Click here
P63004 View 3D Structure Click here
P63005 View 3D Structure Click here
P69566 View 3D Structure Click here
Q03825 View 3D Structure Click here
Q0D730 View 3D Structure Click here
Q0JBT9 View 3D Structure Click here
Q10446 View 3D Structure Click here
Q10A93 View 3D Structure Click here
Q10PG5 View 3D Structure Click here
Q54BK4 View 3D Structure Click here
Q54CT2 View 3D Structure Click here
Q54VL8 View 3D Structure Click here
Q54X16 View 3D Structure Click here
Q59QW5 View 3D Structure Click here
Q5VRV5 View 3D Structure Click here
Q5ZBP7 View 3D Structure Click here
Q6K3E4 View 3D Structure Click here
Q6PC55 View 3D Structure Click here
Q6VN19 View 3D Structure Click here
Q6VN20 View 3D Structure Click here
Q6YDN8 View 3D Structure Click here
Q7KNS3 View 3D Structure Click here
Q7T394 View 3D Structure Click here
Q803D2 View 3D Structure Click here
Q84WK5 View 3D Structure Click here
Q8BHJ5 View 3D Structure Click here
Q8I0F4 View 3D Structure Click here
Q8IET1 View 3D Structure Click here
Q8IYT4 View 3D Structure Click here
Q8SZN4 View 3D Structure Click here
Q95RJ9 View 3D Structure Click here
Q96S59 View 3D Structure Click here
Q9BQ87 View 3D Structure Click here
Q9BZK7 View 3D Structure Click here
Q9D3R6 View 3D Structure Click here
Q9D7M1 View 3D Structure Click here
Q9FN19 View 3D Structure Click here
Q9FUY2 View 3D Structure Click here
Q9M086 View 3D Structure Click here
Q9NDC9 View 3D Structure Click here
Q9NWU2 View 3D Structure Click here
Q9P785 View 3D Structure Click here
Q9QXE7 View 3D Structure Click here
Q9UAU3 View 3D Structure Click here
Q9URU9 View 3D Structure Click here
Q9V3N5 View 3D Structure Click here
Q9VF40 View 3D Structure Click here
Q9VWS1 View 3D Structure Click here