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.
0  structures 861  species 0  interactions 2270  sequences 17  architectures

Family: LIM_bind (PF01803)

Summary: LIM-domain binding protein

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 "LIM domain-binding protein family". More...

LIM domain-binding protein family Edit Wikipedia article

LIM-domain binding protein
Identifiers
Symbol LIM_bind
Pfam PF01803
InterPro IPR002691
SCOP 1j2o
SUPERFAMILY 1j2o

In molecular biology, the LIM domain-binding protein family is a family of proteins which binds to the LIM domain of LIM homeodomain proteins which are transcriptional regulators of development.

Examples

Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) is located in the nuclei of neuronal cells during development, it is co-expressed with ISL1 in early motor neuron differentiation and has a suggested role in the ISL1 dependent development of motor neurons.[1] It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development.[2] The Drosophila melanogaster protein Chip is required for segmentation and activity of a remote wing margin enhancer.[3] Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development.[3] It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions.[3]

References

  1. ^ Jurata LW, Kenny DA, Gill GN (October 1996). "Nuclear LIM interactor, a rhombotin and LIM homeodomain interacting protein, is expressed early in neuronal development". Proc. Natl. Acad. Sci. U.S.A. 93 (21): 11693–8. doi:10.1073/pnas.93.21.11693. PMC 38120Freely accessible. PMID 8876198. 
  2. ^ Bach I, Carriere C, Ostendorff HP, Andersen B, Rosenfeld MG (June 1997). "A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins". Genes Dev. 11 (11): 1370–80. doi:10.1101/gad.11.11.1370. PMID 9192866. 
  3. ^ a b c Morcillo P, Rosen C, Baylies MK, Dorsett D (October 1997). "Chip, a widely expressed chromosomal protein required for segmentation and activity of a remote wing margin enhancer in Drosophila". Genes Dev. 11 (20): 2729–40. doi:10.1101/gad.11.20.2729. PMC 316608Freely accessible. PMID 9334334. 

This article incorporates text from the public domain Pfam and InterPro IPR002691

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.

LIM-domain binding protein Provide feedback

The LIM-domain binding protein, binds to the LIM domain PF00412 of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) P70662 is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons [4]. It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development [2]. The Drosophila protein Chip O18353 is required for segmentation and activity of a remote wing margin enhancer [1]. Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development [1]. It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions [1].

Literature references

  1. Morcillo P, Rosen C, Baylies MK, Dorsett D; , Genes Dev 1997;11:2729-2740.: Chip, a widely expressed chromosomal protein required for segmentation and activity of a remote wing margin enhancer in Drosophila. PUBMED:9334334 EPMC:9334334

  2. Bach I, Carriere C, Ostendorff HP, Andersen B, Rosenfeld MG; , Genes Dev 1997;11:1370-1380.: A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins. PUBMED:9192866 EPMC:9192866

  3. Agulnick AD, Taira M, Breen JJ, Tanaka T, Dawid IB, Westphal H; , Nature 1996;384:270-272.: Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins. PUBMED:8918878 EPMC:8918878

  4. Jurata LW, Kenny DA, Gill GN; , Proc Natl Acad Sci U S A 1996;93:11693-11698.: Nuclear LIM interactor, a rhombotin and LIM homeodomain interacting protein, is expressed early in neuronal development. PUBMED:8876198 EPMC:8876198


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR029005

This entry includes the LIM-domain binding proteins and similar proteins, such as protein Chip from Drosophila, SEUSS from Arabidopsis and Adn1 from fission yeasts.

The LIM-domain binding protein, binds to the LIM domain of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons [PUBMED:8876198]. It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors, both of which have essential roles in development [PUBMED:9192866].

The Drosophila protein Chip (SWISSPROT) is required for segmentation and activity of a remote wing margin enhancer [PUBMED:9334334]. Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development. It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions [PUBMED:9334334].

SEUSS is a transcriptional corepressor from Arabidopsis thaliana [PUBMED:15277686]. SEUSS contains two glutamine-rich domains and a highly conserved domain that shares sequence identity with the dimerisation domain of the LIM-domain-binding transcription co-regulators in animals [PUBMED:11782418].

Several proteins in this entry are transcriptional regulators in fungi. In fission yeasts, adhesion defective protein 1 (Adn1) is a probable transcriptional regulator involved in cell adhesion [PUBMED:19542312]. In Aspergillus fumigatus, the transcriptional activator ptaB forms a complex with somA to control biofilm formation [PUBMED:26529322]. In Candida albicans, MFG1 (morphogenetic regulator of filamentous growth protein 1) has a role in all morphogenetically distinct forms of filamentous growth, including invasive growth and biofilm formation, probably by forming a complex with FLO8 and MSS1 which binds the promoter of the FLO11 gene [PUBMED:22984072].

Domain organisation

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

Loading domain graphics...

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(98)
Full
(2270)
Representative proteomes UniProt
(3230)
NCBI
(5552)
Meta
(0)
RP15
(408)
RP35
(985)
RP55
(1511)
RP75
(1810)
Jalview View  View  View  View  View  View  View  View   
HTML View  View               
PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(98)
Full
(2270)
Representative proteomes UniProt
(3230)
NCBI
(5552)
Meta
(0)
RP15
(408)
RP35
(985)
RP55
(1511)
RP75
(1810)
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
(98)
Full
(2270)
Representative proteomes UniProt
(3230)
NCBI
(5552)
Meta
(0)
RP15
(408)
RP35
(985)
RP55
(1511)
RP75
(1810)
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.

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_1352 (release 4.2)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 98
Number in full: 2270
Average length of the domain: 176.00 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 35.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.2 24.2
Trusted cut-off 24.2 24.4
Noise cut-off 24.1 24.1
Model length: 241
Family (HMM) version: 16
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.