Summary: Pentatricopeptide repeat domain
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Pentatricopeptide repeat Edit Wikipedia article
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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 and by the relative lack of introns in the genes coding for them.
Approximately 450 such proteins have been identified in the arabidopsis genome, and another 477 in the rice genome. 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.
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 and that they are possibly involved in RNA editing. However many trans proteins are required for this editing to occur and research continues to look at which proteins are needed.
Human genes encoding proteins containing this repeat include:
- 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.
- 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.
- 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.
- 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.
- 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.
- 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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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
|Similarity to PfamA using HHSearch:||PPR PPR_1 PPR_2|
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].
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.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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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 127 members:Adaptin_N Alkyl_sulf_dimr ANAPC3 ANAPC5 API5 Arm Arm_2 Arm_3 Avirulence BTAD CAS_CSE1 ChAPs CLASP_N Clathrin Clathrin-link Clathrin_propel Cnd1 Cnd3 Coatomer_E Cohesin_HEAT Cohesin_load COPI_C CRM1_C Cse1 DNA_alkylation Drf_FH3 Drf_GBD DUF1822 DUF2225 DUF3385 DUF3458 DUF3808 DUF3856 DUF4042 DUF924 EST1 EST1_DNA_bind FAT Fis1_TPR_C Fis1_TPR_N Foie-gras_1 GUN4_N HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HemY_N IBB IBN_N IFRD KAP Leuk-A4-hydro_C LRV LRV_FeS MA3 MIF4G MIF4G_like MIF4G_like_2 Mo25 MRP-S27 NARP1 Neurochondrin Nipped-B_C Nro1 NSF Paf67 ParcG PC_rep PHAT PI3Ka PknG_TPR PPP5 PPR PPR_1 PPR_2 PPR_3 PPTA Proteasom_PSMB PUF Rab5-bind Rapsyn_N RPN7 Sel1 SHNi-TPR SNAP SPO22 SRP_TPR_like ST7 Suf SusD SusD-like SusD-like_2 SusD-like_3 TAF6_C TAtT Tcf25 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_3 TPR_4 TPR_5 TPR_6 TPR_7 TPR_8 TPR_9 Upf2 V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps39_1 W2 Xpo1 YfiO
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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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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