Summary: Leucine Rich repeats (2 copies)
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Leucine-rich repeat Edit Wikipedia article
An example of a leucine-rich repeat protein, a porcine ribonuclease inhibitor
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| Identifiers | |||||||||
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| Symbol | LRR_1 | ||||||||
| Pfam | PF00560 | ||||||||
| Pfam clan | CL0022 | ||||||||
| InterPro | IPR001611 | ||||||||
| SCOP | 2bnh | ||||||||
| SUPERFAMILY | 2bnh | ||||||||
| OPM protein | 1xwd | ||||||||
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| Leucine rich repeat variant | |||||||||
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a leucine-rich repeat variant with a novel repetitive protein structural motif
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| Identifiers | |||||||||
| Symbol | LRV | ||||||||
| Pfam | PF01816 | ||||||||
| Pfam clan | CL0020 | ||||||||
| InterPro | IPR004830 | ||||||||
| SCOP | 1lrv | ||||||||
| SUPERFAMILY | 1lrv | ||||||||
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| LRR adjacent | |||||||||
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internalin h: crystal structure of fused n-terminal domains.
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| Identifiers | |||||||||
| Symbol | LRR_adjacent | ||||||||
| Pfam | PF08191 | ||||||||
| InterPro | IPR012569 | ||||||||
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| Leucine rich repeat N-terminal domain | |||||||||
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dimeric bovine tissue-extracted decorin, crystal form 2
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| Identifiers | |||||||||
| Symbol | LRRNT | ||||||||
| Pfam | PF01462 | ||||||||
| InterPro | IPR000372 | ||||||||
| SMART | LRRNT | ||||||||
| SCOP | 1m10 | ||||||||
| SUPERFAMILY | 1m10 | ||||||||
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| Leucine rich repeat N-terminal domain | |||||||||
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the crystal structure of pgip (polygalacturonase inhibiting protein), a leucine rich repeat protein involved in plant defense
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| Identifiers | |||||||||
| Symbol | LRRNT_2 | ||||||||
| Pfam | PF08263 | ||||||||
| InterPro | IPR013210 | ||||||||
| SMART | LRRNT | ||||||||
| SCOP | 1m10 | ||||||||
| SUPERFAMILY | 1m10 | ||||||||
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| Leucine rich repeat C-terminal domain | |||||||||
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third lrr domain of drosophila slit
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| Identifiers | |||||||||
| Symbol | LRRCT | ||||||||
| Pfam | PF01463 | ||||||||
| InterPro | IPR000483 | ||||||||
| SMART | LRRCT | ||||||||
| SCOP | 1m10 | ||||||||
| SUPERFAMILY | 1m10 | ||||||||
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| LRV protein FeS4 cluster | |||||||||
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a leucine-rich repeat variant with a novel repetitive protein structural motif
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| Identifiers | |||||||||
| Symbol | LRV_FeS | ||||||||
| Pfam | PF05484 | ||||||||
| Pfam clan | CL0020 | ||||||||
| InterPro | IPR008665 | ||||||||
| SCOP | 1lrv | ||||||||
| SUPERFAMILY | 1lrv | ||||||||
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A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold.[1][2] It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. 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 tightly sterically packed with leucine residues.
Leucine-rich repeats are frequently involved in the formation of protein–protein interactions.[3][4]
Contents
Examples
Leucine-rich repeat motifs have been identified in a large number of functionally unrelated proteins.[5] The best-known example is the ribonuclease inhibitor, but other proteins such as the tropomyosin regulator tropomodulin and the toll-like receptor also share the motif. In fact, the toll-like receptor possesses 10 successive LRR motifs which serve to bind pathogen- and danger-associated molecular patterns.
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.
One leucine-rich repeat variant domain (LRV) has a novel repetitive structural motif consisting of alternating alpha- and 310-helices arranged in a right-handed superhelix, with the absence of the beta-sheets present in other leucine-rich repeats.[6]
Associated domains
Leucine-rich repeats are often flanked by N-terminal and C-terminal cysteine-rich domains, but not always as is the case with C5orf36
They also co-occur with LRR adjacent domains. These are small, all beta strand domains, which have been structurally described for the protein Internalin (InlA) and related proteins InlB, InlE, InlH from the pathogenic bacterium Listeria monocytogenes. Their function appears to be mainly structural: They are fused to the C-terminal end of leucine-rich repeats, significantly stabilising the LRR, and forming a common rigid entity with the LRR. They are themselves not involved in protein-protein-interactions but help to present the adjacent LRR-domain for this purpose. These domains belong to the family of Ig-like domains in that they consist of two sandwiched beta sheets that follow the classical connectivity of Ig-domains. The beta strands in one of the sheets is, however, much smaller than in most standard Ig-like domains, making it somewhat of an outlier.[7][8][9]
An iron sulphur cluster is found at the N-terminus of some proteins containing the leucine-rich repeat variant domain (LRV). These proteins have a two-domain structure, composed of a small N-terminal domain containing a cluster of four Cysteine residues that houses the 4Fe:4S cluster, and a larger C-terminal domain containing the LRV repeats.[6] Biochemical studies revealed that the 4Fe:4S cluster is sensitive to oxygen, but does not appear to have reversible redox activity.
See also
References
- ^ Kobe B, Deisenhofer J (October 1994). "The leucine-rich repeat: a versatile binding motif". Trends Biochem. Sci. 19 (10): 415–21. doi:10.1016/0968-0004(94)90090-6. PMID 7817399.
- ^ Enkhbayar P, Kamiya M, Osaki M, Matsumoto T, Matsushima N (February 2004). "Structural principles of leucine-rich repeat (LRR) proteins". Proteins. 54 (3): 394–403. doi:10.1002/prot.10605. PMID 14747988.
- ^ Kobe B, Kajava AV (December 2001). "The leucine-rich repeat as a protein recognition motif". Curr. Opin. Struct. Biol. 11 (6): 725–32. doi:10.1016/S0959-440X(01)00266-4. PMID 11751054.
- ^ Gay NJ, Packman LC, Weldon MA, Barna JC (October 1991). "A leucine-rich repeat peptide derived from the Drosophila Toll receptor forms extended filaments with a beta-sheet structure". FEBS Lett. 291 (1): 87–91. doi:10.1016/0014-5793(91)81110-T. PMID 1657640.
- ^ Rothberg JM, Jacobs JR, Goodman CS, Artavanis-Tsakonas S (December 1990). "slit: an extracellular protein necessary for development of midline glia and commissural axon pathways contains both EGF and LRR domains". Genes Dev. 4 (12A): 2169–87. doi:10.1101/gad.4.12a.2169. PMID 2176636.
- ^ a b Peters JW, Stowell MH, Rees DC (December 1996). "A leucine-rich repeat variant with a novel repetitive protein structural motif". Nat. Struct. Biol. 3 (12): 991–4. doi:10.1038/nsb1296-991. PMID 8946850.
- ^ Schubert WD, Gobel G, Diepholz M, Darji A, Kloer D, Hain T, Chakraborty T, Wehland J, Domann E, Heinz DW (September 2001). "Internalins from the human pathogen Listeria monocytogenes combine three distinct folds into a contiguous internalin domain". J. Mol. Biol. 312 (4): 783–94. doi:10.1006/jmbi.2001.4989. PMID 11575932.
- ^ Schubert WD, Urbanke C, Ziehm T, Beier V, Machner MP, Domann E, Wehland J, Chakraborty T, Heinz DW (December 2002). "Structure of internalin, a major invasion protein of Listeria monocytogenes, in complex with its human receptor E-cadherin". Cell. 111 (6): 825–36. doi:10.1016/S0092-8674(02)01136-4. PMID 12526809.
- ^ Freiberg A, Machner MP, Pfeil W, Schubert WD, Heinz DW, Seckler R (March 2004). "Folding and stability of the leucine-rich repeat domain of internalin B from Listeri monocytogenes". J. Mol. Biol. 337 (2): 453–61. doi:10.1016/j.jmb.2004.01.044. PMID 15003459.
Further reading
- Tooze, John; Brändén, Carl-Ivar (1999). Introduction to Protein Structure (2nd ed.). New York: Garland Publishing. ISBN 0-8153-2305-0.
- Wei T, Gong J, Jamitzky F, Heckl WM, Stark RW, Roessle SC (November 2008). "LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs)". BMC Struct. Biol. 8 (1): 47. doi:10.1186/1472-6807-8-47. PMC 2645405
. PMID 18986514.
External links
- Eukaryotic Linear Motif resource motif class LIG_SCF_Skp2-Cks1_1
- SCOP LRR fold
- CATH Alpha-beta horseshoe architecture
- LRRML: a conformational database of leucine-rich repeats
This article incorporates text from the public domain Pfam and InterPro IPR012569
This article incorporates text from the public domain Pfam and InterPro IPR013210
This article incorporates text from the public domain Pfam and InterPro IPR000372
This article incorporates text from the public domain Pfam and InterPro IPR000483
This article incorporates text from the public domain Pfam and InterPro IPR004830
This article incorporates text from the public domain Pfam and InterPro IPR004830
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
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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
| SCOOP: | LRR_1 LRR_5 LRR_6 LRR_8 LRR_9 |
| Similarity to PfamA using HHSearch: | LRR_8 LRR_8 LRR_9 |
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.
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 11 members:
DUF285 FNIP LRR_1 LRR_2 LRR_3 LRR_4 LRR_5 LRR_6 LRR_8 LRR_9 Recep_L_domainAlignments
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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| Seed (276) |
Full (6525) |
Representative proteomes | UniProt (15059) |
NCBI (82328) |
Meta (679) |
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| RP15 (1815) |
RP35 (3737) |
RP55 (5571) |
RP75 (7208) |
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| Jalview | |||||||||
| HTML | |||||||||
| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (276) |
Full (6525) |
Representative proteomes | UniProt (15059) |
NCBI (82328) |
Meta (679) |
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| RP15 (1815) |
RP35 (3737) |
RP55 (5571) |
RP75 (7208) |
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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.
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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.
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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: | Jackhmmer:Q187Q2 |
| Previous IDs: | none |
| Type: | Repeat |
| Author: | Bateman A |
| Number in seed: | 276 |
| Number in full: | 6525 |
| Average length of the domain: | 44.10 aa |
| Average identity of full alignment: | 30 % |
| Average coverage of the sequence by the domain: | 8.78 % |
HMM information
| HMM build commands: |
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 43 | ||||||||||||
| Family (HMM) version: | 6 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Interactions
There are 15 interactions for this family. More...
CAF1 E1_DerP2_DerF2 RnaseA LRR_adjacent TIG LRR_8 LRR_6 LRR_1 LRR_6 LRR_8 Internalin_N PSI LRR_adjacent LRR_4 CadherinStructures
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 217 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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