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14  structures 318  species 0  interactions 1403  sequences 36  architectures

Family: La (PF05383)

Summary: La domain

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La domain Edit Wikipedia article

La domain
PDB 2cqk EBI.jpg
solution structure of the la domain of c-mpl binding protein
Identifiers
Symbol La
Pfam PF05383
InterPro IPR006630
SMART TSPN
PROSITE PDOC00280
MEROPS I75
SCOP 2mpr
SUPERFAMILY 2mpr
TCDB 1.B.3
CDD cd07323

In molecular biology, the La domain is a conserved protein domain.

Human 60 kDa SS-A/Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La. The La protein is a 47 kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome.[1] In the nucleus, La acts as a RNA polymerase III (RNAP III) transcription factor, while in the cytoplasm, La acts as a translation factor.[2] In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation.[3] In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis.[4] The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and an RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif.[5]

Homologous La domain-containing proteins have been identified in a wide range of organisms except Archaea, bacteria and viruses.[6]

References[edit]

  1. ^ Izumi RE, Das S, Barat B, Raychaudhuri S, Dasgupta A (April 2004). "A peptide from autoantigen La blocks poliovirus and hepatitis C virus cap-independent translation and reveals a single tyrosine critical for La RNA binding and translation stimulation". J. Virol. 78 (7): 3763–76. PMC 371053. PMID 15016896. 
  2. ^ Intine RV, Tenenbaum SA, Sakulich AL, Keene JD, Maraia RJ (November 2003). "Differential phosphorylation and subcellular localization of La RNPs associated with precursor tRNAs and translation-related mRNAs". Mol. Cell 12 (5): 1301–7. doi:10.1016/S1097-2765(03)00429-5. PMID 14636586. 
  3. ^ Alfano C, Sanfelice D, Babon J, Kelly G, Jacks A, Curry S, Conte MR (April 2004). "Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein". Nat. Struct. Mol. Biol. 11 (4): 323–9. doi:10.1038/nsmb747. PMID 15004549. 
  4. ^ Keene JD (December 2003). "Posttranscriptional generation of macromolecular complexes". Mol. Cell 12 (6): 1347–9. doi:10.1016/S1097-2765(03)00496-9. PMID 14690589. 
  5. ^ Kenan DJ, Keene JD (April 2004). "La gets its wings". Nat. Struct. Mol. Biol. 11 (4): 303–5. doi:10.1038/nsmb0404-303. PMID 15048103. 
  6. ^ Lin-Marq N, Clarkson SG (January 1995). "A yeast RNA binding protein that resembles the human autoantigen La". J. Mol. Biol. 245 (2): 81–5. doi:10.1006/jmbi.1994.0008. PMID 7799435. 

This article incorporates text from the public domain Pfam and InterPro IPR006630

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.

La domain Provide feedback

This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins [1]. The function of this region is uncertain.

Literature references

  1. Yoo CJ, Wolin SL; , Mol Cell Biol 1994;14:5412-5424.: La proteins from Drosophila melanogaster and Saccharomyces cerevisiae: a yeast homolog of the La autoantigen is dispensable for growth. PUBMED:8035818 EPMC:8035818


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006630

Human Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La. The La protein is a 47 kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome [PUBMED:15016896]. In the nucleus, La acts as a RNA polymerase III (RNAP III) transcription factor, while in the cytoplasm, La acts as a translation factor [PUBMED:14636586]. In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation [PUBMED:15004549]. In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis [PUBMED:14690589]. The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and a RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif [PUBMED:15048103].

Homologous La domain-containing proteins have been identified in a wide range of organisms except Archaea, bacteria and viruses [PUBMED:7799435].

Domain organisation

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Alignments

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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
(33)
Full
(1403)
Representative proteomes NCBI
(1319)
Meta
(11)
RP15
(260)
RP35
(430)
RP55
(669)
RP75
(875)
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Format an alignment

  Seed
(33)
Full
(1403)
Representative proteomes NCBI
(1319)
Meta
(11)
RP15
(260)
RP35
(430)
RP55
(669)
RP75
(875)
Alignment:
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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
(33)
Full
(1403)
Representative proteomes NCBI
(1319)
Meta
(11)
RP15
(260)
RP35
(430)
RP55
(669)
RP75
(875)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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

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Curation View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 33
Number in full: 1403
Average length of the domain: 58.80 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 10.47 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 23.3 21.9
Noise cut-off 20.8 21.2
Model length: 61
Family (HMM) version: 12
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 La domain has been found. There are 14 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 seqence.

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