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180  structures 2137  species 0  interactions 14031  sequences 1605  architectures

Family: LRR_4 (PF12799)

Summary: Leucine Rich repeats (2 copies)

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This is the Wikipedia entry entitled "Leucine-rich repeat". More...

Leucine-rich repeat Edit Wikipedia article

An example of a leucine-rich repeat protein, a porcine ribonuclease inhibitor (PDB ID 2BNH).

A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20-30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tighly sterically packed with leucine residues.

Examples

Leucine-rich repeat motifs have been identified in a large number of functionally unrelated proteins. The best-known example is the ribonuclease inhibitor, but other proteins such as the tropomyosin regulator tropomodulin also share the motif.

Although the canonical LRR protein contains approximately one helix for every beta strand, variants that form beta-alpha superhelix folds sometimes have long loops rather than helices linking successive beta strands.

External links

References

  • Branden C, Tooze J. (1999). Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY.

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.

Leucine Rich repeats (2 copies) Provide feedback

Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.

Literature references

  1. Kobe B, Deisenhofer J; , Trends Biochem Sci 1994;19:415-421.: The leucine-rich repeat: a versatile binding motif. PUBMED:7817399 EPMC:7817399


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025875

This entry represents 2 copies of a leucine rich repeat.

Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each leucine rich repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine rich repeats are often flanked by cysteine rich domains [ PUBMED:7817399 ].

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 LRR (CL0022), which has the following description:

Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains. This Pfam entry contains Leucine Rich Repeats not recognised by the Pfam:PF00560 model.

The clan contains the following 18 members:

DUF285 FBXL18_LRR FNIP LRR_1 LRR_10 LRR_11 LRR_12 LRR_2 LRR_3 LRR_4 LRR_5 LRR_6 LRR_8 LRR_9 LRR_RI_capping Recep_L_domain Transp_inhibit TTSSLRR

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
(245)
Full
(14031)
Representative proteomes UniProt
(38836)
RP15
(3046)
RP35
(6688)
RP55
(11487)
RP75
(15913)
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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
(245)
Full
(14031)
Representative proteomes UniProt
(38836)
RP15
(3046)
RP35
(6688)
RP55
(11487)
RP75
(15913)
Alignment:
Format:
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Sequence:
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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
(245)
Full
(14031)
Representative proteomes UniProt
(38836)
RP15
(3046)
RP35
(6688)
RP55
(11487)
RP75
(15913)
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: Jackhmmer:Q187Q2
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Bateman A
Number in seed: 245
Number in full: 14031
Average length of the domain: 44.2 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 8.24 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 43
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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...

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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 LRR_4 domain has been found. There are 180 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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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
A0A044VDX9 View 3D Structure Click here
A0A044VI90 View 3D Structure Click here
A0A077ZB52 View 3D Structure Click here
A0A0H5S6G0 View 3D Structure Click here
A0A0K0E6R0 View 3D Structure Click here
A0A0K0ENM9 View 3D Structure Click here
A0A0K0JS32 View 3D Structure Click here
A0A0N4U513 View 3D Structure Click here
A0A0N4U5E7 View 3D Structure Click here
A0A0N4UMP3 View 3D Structure Click here
A0A0P0VUV4 View 3D Structure Click here
A0A0P0WYI2 View 3D Structure Click here
A0A0P0WYK8 View 3D Structure Click here
A0A0P0XZB3 View 3D Structure Click here
A0A0R0F4Q7 View 3D Structure Click here
A0A0R0FER8 View 3D Structure Click here
A0A0R0FYR4 View 3D Structure Click here
A0A0R0FZS5 View 3D Structure Click here
A0A0R0G0Q1 View 3D Structure Click here
A0A0R0G173 View 3D Structure Click here
A0A0R0G382 View 3D Structure Click here
A0A0R0GIZ1 View 3D Structure Click here
A0A0R0GRU2 View 3D Structure Click here
A0A0R0GYX9 View 3D Structure Click here
A0A0R0HLC5 View 3D Structure Click here
A0A0R0HSM1 View 3D Structure Click here
A0A0R0KCP0 View 3D Structure Click here
A0A0R4J3Q4 View 3D Structure Click here
A0A175WGB9 View 3D Structure Click here
A0A1C1CZA8 View 3D Structure Click here
A0A1D6E248 View 3D Structure Click here
A0A1D6GJ33 View 3D Structure Click here
A0A1D6IXB1 View 3D Structure Click here
A0A1D6KTS2 View 3D Structure Click here
A0A1D6NCX4 View 3D Structure Click here
A0A1D6NLS2 View 3D Structure Click here
A0A1D8PTY3 View 3D Structure Click here
A0A3P7DE91 View 3D Structure Click here
A0A3P7EK84 View 3D Structure Click here
A0A3P7GBD1 View 3D Structure Click here