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0  structures 468  species 0  interactions 31410  sequences 3797  architectures

Family: PPR (PF01535)

Summary: PPR repeat

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This is the Wikipedia entry entitled "Pentatricopeptide repeat". More...

Pentatricopeptide repeat Edit Wikipedia article

Pentatricopeptide repeat
Identifiers
Symbol PPR
Pfam PF01535
Pfam clan CL0020
InterPro IPR002885
PROSITE PS51375

The pentatricopeptide repeat (PPR) is a 35-amino acid sequence motif. Pentatricopeptide repeat containing proteins are a family of proteins commonly found in the plant kingdom. They are distinguished by the presence of tandem degenerate PPR motifs[1] and by the relative lack of introns in the genes coding for them.[2]

Approximately 450 such proteins have been identified in the arabidopsis genome, and another 477 in the rice genome.[3] Despite the large size of the protein family, genetic data suggest that there is little or no redundancy of function between the PPR proteins in arabidopsis.[2]

The purpose of PPR proteins is currently under dispute. It has been shown that a good deal of those in Arabidopsis interact (often essentially) with mitochondria and other organelles[2] and that they are possibly involved in RNA editing.[4] However many trans proteins are required for this editing to occur and research continues to look at which proteins are needed.[5]

The structure of the PPR has not yet been determined, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat.[6]

Examples

Human genes encoding proteins containing this repeat include:

References

  1. ^ Mingler MK, Hingst AM, Clement SL, Yu LE, Reifur L, Koslowsky DJ (November 2006). "Identification of pentatricopeptide repeat proteins in Trypanosoma brucei". Mol. Biochem. Parasitol. 150 (1): 37–45. doi:10.1016/j.molbiopara.2006.06.006. PMID 16837079. 
  2. ^ a b c Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, Szurek B, Taconnat L, Small I (August 2004). "Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis". Plant Cell 16 (8): 2089–103. doi:10.1105/tpc.104.022236. PMC 519200. PMID 15269332. 
  3. ^ O'Toole N, Hattori M, Andres C, Iida K, Lurin C, Schmitz-Linneweber C, Sugita M, Small I (June 2008). "On the expansion of the pentatricopeptide repeat gene family in plants". Mol. Biol. Evol. 25 (6): 1120–8. doi:10.1093/molbev/msn057. PMID 18343892. 
  4. ^ Kotera E, Tasaka M, Shikanai T (January 2005). "A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts". Nature 433 (7023): 326–30. doi:10.1038/nature03229. PMID 15662426. 
  5. ^ Takenaka M, Verbitskiy D, Zehrmann A, Brennicke A (June 2010). "Reverse genetic screening identifies five E-class PPR-proteins involved in RNA editing in mitochondria of Arabidopsis Thaliana". J Biol Chem 285 (35): 27122–27129. doi:10.1074/jbc.M110.128611. PMC 2930711. PMID 20566637. 
  6. ^ Small ID, Peeters N (February 2000). "The PPR motif - a TPR-related motif prevalent in plant organellar proteins". Trends Biochem. Sci. 25 (2): 46–7. doi:10.1016/s0968-0004(99)01520-0. PMID 10664580. 


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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.

PPR repeat Provide feedback

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 P32522 that may be involved in RNA stabilisation [1]. This domain occurs in crp1 that is involved in RNA processing [2]. This repeat is associated with a predicted plant protein O49549 that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR [3].

Literature references

  1. Manthey GM, McEwen JE; , EMBO J 1995;14:4031-4043.: The product of the nuclear gene PET309 is required for translation of mature mRNA and stability or production of intron-containing RNAs derived from the mitochondrial COX1 locus of Saccharomyces cerevisiae. PUBMED:7664742 EPMC:7664742

  2. Barkan A, Walker M, Nolasco M, Johnson D; , EMBO J 1994;13:3170-3181.: A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms. PUBMED:8039510 EPMC:8039510

  3. Small ID, Peeters I; , Trends Biochem Sci 2000;25:45-47.: The PPR motif - a TPR-related motif prevalent in plant organellar proteins. PUBMED:10664580 EPMC:10664580


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002885

This entry represents the PPR repeat.

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif [PUBMED:10664580]. Most of PPR proteins have roles in mitochondria or plastid [PUBMED:15270678]. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [PUBMED:10664580, PUBMED:15269332]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [PUBMED:12782738, PUBMED:12832482, PUBMED:18031283]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins.

Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PROSITEDOC) [PUBMED:10664580].

The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [PUBMED:15269332, PUBMED:17560114].

Examples of PPR repeat-containing proteins include PET309 SWISSPROT, which may be involved in RNA stabilisation [PUBMED:7664742], and crp1, which is involved in RNA processing [PUBMED:8039510]. The repeat is associated with a predicted plant protein SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(518)
Full
(31410)
Representative proteomes NCBI
(82367)
Meta
(965)
RP15
(2628)
RP35
(15898)
RP55
(19987)
RP75
(23088)
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Format an alignment

  Seed
(518)
Full
(31410)
Representative proteomes NCBI
(82367)
Meta
(965)
RP15
(2628)
RP35
(15898)
RP55
(19987)
RP75
(23088)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(518)
Full
(31410)
Representative proteomes NCBI
(82367)
Meta
(965)
RP15
(2628)
RP35
(15898)
RP55
(19987)
RP75
(23088)
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.

HMM logo

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Trees

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Note: You can also download the data file for the tree.

Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_874 (release 4.0)
Previous IDs: DUF17;
Type: Family
Author: Bateman A, Birney E
Number in seed: 518
Number in full: 31410
Average length of the domain: 29.30 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 15.97 %

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 9.3
Trusted cut-off 25.0 9.3
Noise cut-off 24.9 9.2
Model length: 31
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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