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26  structures 1390  species 0  interactions 241615  sequences 13775  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
Pfam clanCL0020

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 been resolved. It folds into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat. Several repeats of the protein forms a ring around a single-strand RNA molecule in a sequence-sensitive way reminiscent of TAL effectors.[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. ^ Yin P, Li Q, Yan C, Liu Y, Liu J, Yu F, et al. (December 2013). "Structural basis for the modular recognition of single-stranded RNA by PPR proteins". Nature. 504 (7478): 168–71. doi:10.1038/nature12651. PMID 24162847.

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.

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

Internal 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 ]. PPR proteins are sequence-specific RNA-binding proteins that are involved in multiple aspects of RNA metabolism [ PUBMED:18031283 , PUBMED:22576772 ]. They can bind a diversity of sequences that confers the variability in its functions [ PUBMED:30125002 ]. Most have roles in mitochondria or plastids [ 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 [ PUBMED:12782738 , PUBMED:12832482 ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins.

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

The crystal structure of maize chloroplast PPR10 has been reported. The nineteen repeats of PPR10 are assembled into a right-handed superhelical spiral. PPR10 forms a homodimer and exhibits considerable conformational changes upon binding to its ssRNA target, with six nucleotides being specifically recognized by six corresponding PPR10 repeats [ PUBMED:24162847 ].

Domain organisation

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

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Pfam Clan

This family is a member of clan TPR (CL0020), which has the following description:

Tetratricopeptide-like repeats are found in a numerous and diverse proteins involved in such functions as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The clan contains the following 176 members:

Adaptin_N Alkyl_sulf_dimr ANAPC3 ANAPC5 ANAPC8 APC_rep API5 Arm Arm_2 Arm_3 Arm_vescicular Atx10homo_assoc B56 BAF250_C BTAD CAS_CSE1 ChAPs CHIP_TPR_N CID CLASP_N Clathrin Clathrin-link Clathrin_H_link Clathrin_propel Cnd1 Cnd3 Coatomer_E Cohesin_HEAT Cohesin_load ComR_TPR COPI_C CPL CRM1_C CRM1_repeat CRM1_repeat_3 Cse1 CTK3 DHR-2 DIL DNA_alkylation Dopey_N Drf_FH3 Drf_GBD DUF1822 DUF2019 DUF2225 DUF3385 DUF3458_C DUF3808 DUF3856 DUF4042 DUF5588 DUF5691 DUF6340 DUF6377 DUF924 EAD11 EST1 EST1_DNA_bind FAT Fis1_TPR_C Fis1_TPR_N Foie-gras_1 GUN4_N HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HEAT_UF HemY_N HrpB1_HrpK HSM3_C HSM3_N IBB IBN_N IFRD Importin_rep Importin_rep_2 Importin_rep_3 Importin_rep_4 Importin_rep_5 Importin_rep_6 Insc_C KAP Leuk-A4-hydro_C LRV LRV_FeS MA3 MIF4G MIF4G_like MIF4G_like_2 MMS19_C Mo25 MRP-S27 Mtf2 NARP1 Neurochondrin Nipped-B_C Nro1 NSF Paf67 ParcG PC_rep PHAT PI3Ka PknG_TPR PPP5 PPR PPR_1 PPR_2 PPR_3 PPR_long PPTA Proteasom_PSMB PUF Rapsyn_N RIX1 RNPP_C RPM2 RPN7 Sel1 SHNi-TPR SNAP SPO22 SRP_TPR_like ST7 Suf SusD-like SusD-like_2 SusD-like_3 SusD_RagB SYCP2_ARLD TAF6_C TAL_effector TAtT Tcf25 TIP120 TOM20_plant TPR_1 TPR_10 TPR_11 TPR_12 TPR_14 TPR_15 TPR_16 TPR_17 TPR_18 TPR_19 TPR_2 TPR_20 TPR_21 TPR_22 TPR_3 TPR_4 TPR_5 TPR_6 TPR_7 TPR_8 TPR_9 TPR_MalT TTC7_N UNC45-central Upf2 V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps39_1 W2 WSLR Wzy_C_2 Xpo1 YcaO_C YfiO Zmiz1_N


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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_874 (release 4.0)
Previous IDs: DUF17;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Birney E
Number in seed: 458
Number in full: 241615
Average length of the domain: 29.30 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 14.69 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 9.3
Trusted cut-off 25.0 9.4
Noise cut-off 24.9 -1000000.0
Model length: 31
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence


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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 domain has been found. There are 26 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 sequence.

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