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1  structure 22  species 1  interaction 23  sequences 5  architectures

Family: SRX (PF09201)

Summary: SRX

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This is the Wikipedia entry entitled "Signal recognition particle receptor". More...

Signal recognition particle receptor Edit Wikipedia article

SRX
PDB 1nrj EBI.jpg
Structure of the beta subunit of the eukaryotic signal recognition particle receptor.[1]
Identifiers
Symbol SRX
Pfam PF09201
InterPro IPR015284
SCOP 1nrj
SUPERFAMILY 1nrj
OPM superfamily 145
OPM protein 1nrj

Signal recognition particle (SRP) receptor, also called docking protein, is a dimer composed of 2 different subunits that are associated exclusively with the rough ER in mammalian cells. Its main function is to identify the SRP units. SRP (signal recognition particle) is a molecule that helps the ribosome-mRNA-polypeptide complexes to settle down on the membrane of the endoplasmic reticulum.

SRP receptor[edit]

The eukaryotic SRP receptor (termed SR) is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain,[2] while the prokaryotic SRP receptor comprises only the monomeric loosely membrane-associated SR-alpha homologue FtsY. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon.[3] SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane.[4] SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel.

This family represents homologues of the alpha subunit of the SR receptor. Members of this entry consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta).[2]

Signal Recognition Particle (SRP)[edit]

The Signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes.[5][6] SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor.[7] In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane.

References[edit]

  1. ^ Schwartz T, Blobel G (March 2003). "Structural basis for the function of the beta subunit of the eukaryotic signal recognition particle receptor". Cell 112 (6): 793–803. doi:10.1016/S0092-8674(03)00161-2. PMID 12654246. 
  2. ^ a b Blobel G, Schwartz T (2003). "Structural basis for the function of the beta subunit of the eukaryotic signal recognition particle receptor". Cell 112 (6): –. doi:10.1016/S0092-8674(03)00161-2. PMID 12654246. 
  3. ^ Andrews DW, Legate KR, Falcone D (2000). "Nucleotide-dependent binding of the GTPase domain of the signal recognition particle receptor beta-subunit to the alpha-subunit". J. Biol. Chem. 275 (35): –. doi:10.1074/jbc.M003215200. PMID 10859309. 
  4. ^ Walter P, Miller JD, Tajima S, Lauffer L (1995). "The beta subunit of the signal recognition particle receptor is a transmembrane GTPase that anchors the alpha subunit, a peripheral membrane GTPase, to the endoplasmic reticulum membrane". J. Cell Biol. 128 (3): –. doi:10.1083/jcb.128.3.273. PMC 2120348. PMID 7844142. 
  5. ^ Stroud RM, Walter P, Rutenber E, Reyes CL (2007). "X-ray Structures of the Signal Recognition Particle Receptor Reveal Targeting Cycle Intermediates". In Zhang, Shuguang. PLoS ONE 2 (7): –. doi:10.1371/journal.pone.0000607. PMC 1904258. PMID 17622352. 
  6. ^ Dobberstein B, High S, Romisch K, Miller FW (2006). "Human autoantibodies against the 54 kDa protein of the signal recognition particle block function at multiple stages". Arthritis Res Ther 8 (2): –. doi:10.1186/ar1895. PMC 1526608. PMID 16469117. 
  7. ^ Walter P, Bradshaw N (2007). "The Signal Recognition Particle (SRP) RNA Links Conformational Changes in the SRP to Protein Targeting". Mol. Biol. Cell 18 (7): –. doi:10.1091/mbc.E07-02-0117. PMC 1924838. PMID 17507650. 

This article incorporates text from the public domain Pfam and InterPro IPR015284

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Members of this family, which are predominantly found in eukaryotic signal recognition particle receptor alpha, consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta) [1].

Literature references

  1. Schwartz T, Blobel G; , Cell. 2003;112:793-803.: Structural basis for the function of the beta subunit of the eukaryotic signal recognition particle receptor. PUBMED:12654246 EPMC:12654246


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015284

The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [PUBMED:17622352, PUBMED:16469117]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor [PUBMED:17507650]. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 [PUBMED:12364595].

The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain [PUBMED:12654246]. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon [PUBMED:10859309]. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane [PUBMED:7844142]. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel.

This entry represents a homologue of the alpha subunit of the SR receptor. Members of this entry consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta) [PUBMED:12654246].

Domain organisation

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Representative proteomes NCBI
(22)
Meta
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RP15
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RP35
(6)
RP55
(12)
RP75
(13)
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  Seed
(5)
Full
(23)
Representative proteomes NCBI
(22)
Meta
(0)
RP15
(1)
RP35
(6)
RP55
(12)
RP75
(13)
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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.

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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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Seed source: pdb_1nrj
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 5
Number in full: 23
Average length of the domain: 149.30 aa
Average identity of full alignment: 57 %
Average coverage of the sequence by the domain: 24.56 %

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 25.0 25.0
Trusted cut-off 26.2 141.3
Noise cut-off 22.0 22.0
Model length: 148
Family (HMM) version: 5
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Species distribution

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Interactions

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SRPRB

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 SRX domain has been found. There are 1 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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