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19  structures 475  species 0  interactions 9588  sequences 105  architectures

Family: L27 (PF02828)

Summary: L27 domain

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This is the Wikipedia entry entitled "L27 domain". More...

L27 domain Edit Wikipedia article

L27 domain
PDB 1rso EBI.jpg
Structure of presynaptic protein SAP97.[1]
Identifiers
SymbolL27
PfamPF02828
InterProIPR014775
L27_1
PDB 1rso EBI.jpg
hetero-tetrameric l27 (lin-2, lin-7) domain complexes as organization platforms of supra-molecular assemblies
Identifiers
SymbolL27_1
PfamPF09058
InterProIPR015143
L27_2
PDB 1vf6 EBI.jpg
2.1 angstrom crystal structure of the pals-1-l27n and patj l27 heterodimer complex
Identifiers
SymbolL27_2
PfamPF09045
InterProIPR015132
L27_N
PDB 1vf6 EBI.jpg
2.1 angstrom crystal structure of the pals-1-l27n and patj l27 heterodimer complex
Identifiers
SymbolL27_N
PfamPF09060
InterProIPR015145

The L27 domain is a protein domain that is found in receptor targeting proteins Lin-2 and Lin-7 (LIN7A, LIN7B, LIN7C), as well as some protein kinases and human MPP2 protein.[2] The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices.[1] The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer.[3]

The L27_N domain is often found at the N-terminus of the L27 domain. It plays a role in the biogenesis of tight junctions and in the establishment of cell polarity in epithelial cells. Each L27_N domain consists of three alpha-helices, the first two of which form an antiparallel coiled-coil. Two L27 domains come together to form a four-helical bundle with the antiparallel coiled-coils formed by the first two helices. The third helix of each domain forms another coiled-coil packing at one end of the four-helix bundle, creating a large hydrophobic interface: the hydrophobic interactions are the major force that drives heterodimer formation.[4]

References

  1. ^ a b Feng W, Long JF, Fan JS, Suetake T, Zhang M (May 2004). "The tetrameric L27 domain complex as an organization platform for supramolecular assemblies" (PDF). Nat. Struct. Mol. Biol. 11 (5): 475–80. doi:10.1038/nsmb751. PMID 15048107.
  2. ^ Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B (July 2000). "L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7". Trends Biochem. Sci. 25 (7): 317–8. doi:10.1016/s0968-0004(00)01599-1. PMID 10871881.
  3. ^ Feng W, Long JF, Zhang M (May 2005). "A unified assembly mode revealed by the structures of tetrameric L27 domain complexes formed by mLin-2/mLin-7 and Patj/Pals1 scaffold proteins". Proc. Natl. Acad. Sci. U.S.A. 102 (19): 6861–6. doi:10.1073/pnas.0409346102. PMC 1100767. PMID 15863617.
  4. ^ Li Y, Karnak D, Demeler B, Margolis B, Lavie A (July 2004). "Structural basis for L27 domain-mediated assembly of signaling and cell polarity complexes". EMBO J. 23 (14): 2723–33. doi:10.1038/sj.emboj.7600294. PMC 514954. PMID 15241471.

Further reading

  • Petrosky KY, Ou HD, Löhr F, Dötsch V, Lim WA (November 2005). "A general model for preferential hetero-oligomerization of LIN-2/7 domains: mechanism underlying directed assembly of supramolecular signaling complexes". J. Biol. Chem. 280 (46): 38528–36. doi:10.1074/jbc.M506536200. PMID 16147993.
This article incorporates text from the public domain Pfam and InterPro: IPR014775
This article incorporates text from the public domain Pfam and InterPro: IPR015143
This article incorporates text from the public domain Pfam and InterPro: IPR015132
This article incorporates text from the public domain Pfam and InterPro: IPR015145


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L27 domain Provide feedback

The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7.

Literature references

  1. Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B; , Trends Biochem Sci 2000;25:317-318.: L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7. PUBMED:10871881 EPMC:10871881


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014775

The L27 domain is found, among others, in receptor targeting proteins Lin-2 and Lin-7 [ PUBMED:10871881 ].

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 L27 (CL0614), which has the following description:

The clan contains the following 5 members:

L27 L27_1 L27_2 L27_N UCH_C

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...

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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
(74)
Full
(9588)
Representative proteomes UniProt
(14036)
RP15
(861)
RP35
(2320)
RP55
(6814)
RP75
(9609)
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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
(74)
Full
(9588)
Representative proteomes UniProt
(14036)
RP15
(861)
RP35
(2320)
RP55
(6814)
RP75
(9609)
Alignment:
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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
(74)
Full
(9588)
Representative proteomes UniProt
(14036)
RP15
(861)
RP35
(2320)
RP55
(6814)
RP75
(9609)
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: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: SMART
Number in seed: 74
Number in full: 9588
Average length of the domain: 52.10 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 12.98 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 53
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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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 L27 domain has been found. There are 19 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
A0A0G2K4N7 View 3D Structure Click here
A0A286Y9N6 View 3D Structure Click here
A0A2R8QIA2 View 3D Structure Click here
A1Z8G0 View 3D Structure Click here
A5PEX5 View 3D Structure Click here
B3DH78 View 3D Structure Click here
B4F7E7 View 3D Structure Click here
D3ZAA9 View 3D Structure Click here
E2QD98 View 3D Structure Click here
E7F7X1 View 3D Structure Click here
F1Q9P1 View 3D Structure Click here
F1QKE3 View 3D Structure Click here
F1QV76 View 3D Structure Click here
F1QWI5 View 3D Structure Click here
F1R2J9 View 3D Structure Click here
F1RDK3 View 3D Structure Click here
O14910 View 3D Structure Click here
O14936 View 3D Structure Click here
O70589 View 3D Structure Click here
O88910 View 3D Structure Click here
O88951 View 3D Structure Click here
O88952 View 3D Structure Click here
O88954 View 3D Structure Click here
P54936 View 3D Structure Click here
Q13368 View 3D Structure Click here
Q14168 View 3D Structure Click here
Q1LW94 View 3D Structure Click here
Q24210 View 3D Structure Click here
Q5T2T1 View 3D Structure Click here
Q5U2Y3 View 3D Structure Click here
Q62915 View 3D Structure Click here
Q6P0D7 View 3D Structure Click here
Q6P7F1 View 3D Structure Click here
Q6PC63 View 3D Structure Click here
Q792I0 View 3D Structure Click here
Q7KT16 View 3D Structure Click here
Q8BVD5 View 3D Structure Click here
Q8IMT8 View 3D Structure Click here
Q8JHF4 View 3D Structure Click here
Q8JZS0 View 3D Structure Click here