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4  structures 591  species 0  interactions 11121  sequences 3381  architectures

Family: PPR_3 (PF13812)

Summary: Pentatricopeptide repeat domain

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

Pentatricopeptide repeat Edit Wikipedia article

Pentatricopeptide repeat
Symbol PPR
Pfam PF01535
Pfam clan CL0020
InterPro IPR002885

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]


Human genes encoding proteins containing this repeat include:


  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.

Pentatricopeptide repeat domain Provide feedback

This family matches additional variants of the PPR repeat that were not captured by the model for PF01535. The exact function is not known.

Internal database links

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

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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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Curation and family details

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Seed source: Jackhmmer:Q9USP3
Previous IDs: none
Type: Repeat
Author: Coggill P
Number in seed: 130
Number in full: 11121
Average length of the domain: 33.00 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 6.71 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 10.0
Trusted cut-off 27.0 10.0
Noise cut-off 26.9 9.9
Model length: 34
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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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 PPR_3 domain has been found. There are 4 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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