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0  structures 26  species 0  interactions 28  sequences 3  architectures

Family: VAR1 (PF05316)

Summary: Mitochondrial ribosomal protein (VAR1)

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This is the Wikipedia entry entitled "Var1 protein domain". More...

Var1 protein domain Edit Wikipedia article

VAR1
Identifiers
Symbol VAR1
Pfam PF05316
InterPro IPR007980


In molecular biology, VAR1 protein domain, otherwise known as variant protein 1, is a ribosomal protein that forms part of the small ribosomal subunit in yeast mitochondria. Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. VAR1 is the only protein in the yeast mitochondrial ribosome to be encoded in the mitochondria - the remaining approximately 80 ribosomal proteins are encoded in the nucleus.[1] VAR1 along with 15S rRNA are necessary for the formation of mature 37S subunits.[2]

Function[edit]

It is thought that Var1 plays a role in the early steps of small subunit assembly and is required for the of incorporation of at least one ribosomal protein. It is important for mitochondrial translational initiation, since it requires the interaction between the small ribosomal subunit and the message-specific translation factors. [1]

Ribosomal proteins in translation[edit]

Ribosomes are the organelles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites.[3][4] Since Var1 helps form the small subunit of the ribosome, its significance become apparent in translation and cell survival.

References[edit]

  1. ^ a b Mason TL, Pan C, Sanchirico ME, Sirum-Connolly K (December 1996). "Molecular genetics of the peptidyl transferase center and the unusual Var1 protein in yeast mitochondrial ribosomes". Experientia 52 (12): 1148–57. PMID 8988258. 
  2. ^ Davis SC, Ellis SR (May 1995). "Incorporation of the yeast mitochondrial ribosomal protein Mrp2 into ribosomal subunits requires the mitochondrially encoded Var1 protein". Mol. Gen. Genet. 247 (3): 379–86. PMID 7770043. 
  3. ^ Ramakrishnan V, Moore PB (April 2001). "Atomic structures at last: the ribosome in 2000". Curr. Opin. Struct. Biol. 11 (2): 144–54. PMID 11297922. 
  4. ^ Maguire BA, Zimmermann RA (March 2001). "The ribosome in focus". Cell 104 (6): 813–6. PMID 11290319. 

This article incorporates text from the public domain Pfam and InterPro IPR007980

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Mitochondrial ribosomal protein (VAR1) Provide feedback

This family consists of the yeast mitochondrial ribosomal proteins VAR1. Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. In yeast the two ribosomal RNAs and a single ribosomal protein, VAR1, are products of mitochondrial genes, and the remaining approximately 80 ribosomal proteins are encoded in the nucleus [1]. VAR1 along with 15S rRNA are necessary for the formation of mature 37S subunits [2].

Literature references

  1. Mason TL, Pan C, Sanchirico ME, Sirum-Connolly K; , Experientia 1996;52:1148-1157.: Molecular genetics of the peptidyl transferase center and the unusual Var1 protein in yeast mitochondrial ribosomes. PUBMED:8988258 EPMC:8988258

  2. Davis SC, Ellis SR; , Mol Gen Genet 1995;247:379-386.: Incorporation of the yeast mitochondrial ribosomal protein Mrp2 into ribosomal subunits requires the mitochondrially encoded Var1 protein. PUBMED:7770043 EPMC:7770043


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007980

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [PUBMED:11297922, PUBMED:11290319]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [PUBMED:11290319, PUBMED:11114498].

This family consists of the VAR1 mitochondrial ribosomal proteins found in yeast. Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. VAR1 is the only protein in the yeast mitochondrial ribosome to be encoded in the mitochondria - the remaining approximately 80 ribosomal proteins are encoded in the nucleus [PUBMED:8988258]. VAR1 along with 15S rRNA are necessary for the formation of mature 37S subunits [PUBMED:7770043].

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(5)
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Representative proteomes NCBI
(39)
Meta
(0)
RP15
(2)
RP35
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RP55
(8)
RP75
(9)
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Seed source: Pfam-B_7802 (release 7.7)
Previous IDs: Yeast_VAR1;
Type: Family
Author: Moxon SJ
Number in seed: 5
Number in full: 28
Average length of the domain: 290.00 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 79.83 %

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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 22.1 22.1
Trusted cut-off 22.4 22.4
Noise cut-off 20.5 22.0
Model length: 350
Family (HMM) version: 7
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