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26  structures 1469  species 0  interactions 253857  sequences 15902  architectures

Family: PPR (PF01535)

Summary: PPR repeat

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Pentatricopeptide repeat Edit Wikipedia article

Pentatricopeptide Repeat (PPR) proteins are a family of proteins commonly found in the plant kingdom. They are distinguished by their repeating 35-amino acid motif[citation needed], and by their relative lack of introns[citation needed].

Approximately 450 such proteins have been identified in the arabidopsis genome[citation needed]. These proteins have been also identified in the rice genome[citation needed].

The purpose of PPR proteins is currently under dispute. It has been shown that a good deal of those in Arabidopsis interact with mitochondria and other organelles[citation needed], and that they are possibly involved in editing RNA[citation needed].

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 252 members:

14-3-3 AAR2 Aconitase_B_N Adaptin_N Alkyl_sulf_dimr ANAPC3 ANAPC5 ANAPC8 Apc1_MidN APC_rep API5 Aquarius_N Arm Arm_2 Arm_3 Arm_vescicular Atx10homo_assoc B56 BAF250_C BRO1 BTAD CAS_CSE1 ChAPs CHIP_TPR_N CID CLASP_N Clathrin Clathrin-link Clathrin_H_link Clathrin_propel Cnd1 Cnd1_N Cnd3 CNOT1_CAF1_bind CNOT1_HEAT_N CNOT1_TTP_bind Coatomer_E Cohesin_HEAT Cohesin_load ComR_TPR COPI_C CPL CRM1_C CRM1_repeat CRM1_repeat_3 Cse1 CTK3 CTNNBL Cullin DHR-2_Lobe_A DHR-2_Lobe_C DIL DNA-PKcs_N DNA_alkylation DNAPKcs_CC1-2 DNAPKcs_CC3 DNAPKcs_CC5 Dopey_N Drf_FH3 Drf_GBD DUF1822 DUF2019 DUF2225 DUF3385 DUF3458_C DUF3730 DUF3856 DUF4042 DUF4704 DUF5071 DUF5106 DUF5588 DUF5691 DUF6340 DUF6377 DUF6584 DUF924 E_motif EAD11 eIF-3c_N ELMO_ARM EST1 EST1_DNA_bind FA_FANCE FANCF FANCI_HD1 FANCI_HD2 FANCI_S1 FANCI_S1-cap FANCI_S2 FANCI_S3 FANCI_S4 FAT Fes1 Fis1_TPR_C Fis1_TPR_N Focadhesin Foie-gras_1 GET4 GLE1 GUN4_N HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HEAT_UF HemY_N HMW1C_N HPS6_C HrpB1_HrpK HSM3_C HSM3_N Hyccin IBB IBN_N IFRD Iml2-TPR_39 Importin_rep Importin_rep_2 Importin_rep_3 Importin_rep_4 Importin_rep_5 Importin_rep_6 Insc_C Ints3_N KAP Kinetochor_Ybp2 Laa1_Sip1_HTR5 Leuk-A4-hydro_C LRV LRV_FeS MA3 Mad3_BUB1_I MAP3K_TRAF_bd MIF4G MIF4G_like MIF4G_like_2 MIX MMS19_C Mo25 MRP-S27 Mtf2 MUN NatA_aux_su Neurobeachin Neurochondrin Nic96 Nipped-B_C Not1 Nro1 NSF Paf67 ParcG PAT1 PC_rep PDS5 Peptidase_M9_N PHAT PI3Ka PknG_TPR PPP5 PPR PPR_1 PPR_2 PPR_3 PPR_long PPTA Proteasom_PSMB PUF PUL RAI16-like Rapsyn_N Rcd1 RIH_assoc RINT1_TIP1 RIX1 RNPP_C RPM2 RPN6_N RPN7 RYDR_ITPR Sel1 SHNi-TPR SIL1 SLT_L SNAP SPO22 SRP_TPR_like ST7 STAG Suf SusD-like SusD-like_2 SusD-like_3 SusD_RagB SYCP2_ARLD SYMPK_PTA1_N TAF1_subA TAF6_C TAL_effector TAP42 TAtT Tcf25 TIP120 TOM20_plant TPR-S 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 Tra1_ring TRF TTC7_N Type_III_YscG UNC45-central Upf2 Uso1_p115_head V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps16_C Vps35 Vps39_1 VPS53_C W2 Wap1 WSLR Wzy_C_2 Xpo1 YcaO_C YfiO Zmiz1_N

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(458)
Full
(253857)
Representative proteomes UniProt
(380234)
RP15
(43923)
RP35
(146337)
RP55
(231810)
RP75
(292455)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(458)
Full
(253857)
Representative proteomes UniProt
(380234)
RP15
(43923)
RP35
(146337)
RP55
(231810)
RP75
(292455)
Alignment:
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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
(458)
Full
(253857)
Representative proteomes UniProt
(380234)
RP15
(43923)
RP35
(146337)
RP55
(231810)
RP75
(292455)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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

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: Repeat
Sequence Ontology: SO:0001068
Author: Bateman A , Birney E
Number in seed: 458
Number in full: 253857
Average length of the domain: 29.3 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 14.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 9.3
Trusted cut-off 25.0 9.5
Noise cut-off 24.9 -1000000.0
Model length: 31
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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Structures

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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A077Z2R3 View 3D Structure Click here
A0A096Q9E4 View 3D Structure Click here
A0A096QEP8 View 3D Structure Click here
A0A096QZD3 View 3D Structure Click here
A0A096R0S2 View 3D Structure Click here
A0A096RDL4 View 3D Structure Click here
A0A096TBR6 View 3D Structure Click here
A0A0D2D9P6 View 3D Structure Click here
A0A0D2GUE3 View 3D Structure Click here
A0A0J9XNE3 View 3D Structure Click here
A0A0N7KCE8 View 3D Structure Click here
A0A0N7KCI8 View 3D Structure Click here
A0A0N7KDH3 View 3D Structure Click here
A0A0N7KPI0 View 3D Structure Click here
A0A0N7KPK3 View 3D Structure Click here
A0A0N7KSD6 View 3D Structure Click here
A0A0N7KTW7 View 3D Structure Click here
A0A0P0UZ80 View 3D Structure Click here
A0A0P0V1C9 View 3D Structure Click here
A0A0P0V1H7 View 3D Structure Click here
A0A0P0V1K3 View 3D Structure Click here
A0A0P0V399 View 3D Structure Click here
A0A0P0V3T7 View 3D Structure Click here
A0A0P0V4P7 View 3D Structure Click here
A0A0P0V4V8 View 3D Structure Click here
A0A0P0V7C6 View 3D Structure Click here
A0A0P0V9J9 View 3D Structure Click here
A0A0P0VBD6 View 3D Structure Click here
A0A0P0VC08 View 3D Structure Click here
A0A0P0VD44 View 3D Structure Click here
A0A0P0VDP7 View 3D Structure Click here
A0A0P0VE04 View 3D Structure Click here
A0A0P0VED0 View 3D Structure Click here
A0A0P0VEJ3 View 3D Structure Click here
A0A0P0VRC2 View 3D Structure Click here
A0A0P0VS67 View 3D Structure Click here
A0A0P0VTK8 View 3D Structure Click here
A0A0P0VVG0 View 3D Structure Click here
A0A0P0VXU3 View 3D Structure Click here
A0A0P0VYI2 View 3D Structure Click here