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Conserved domains on  [gi|334186792|ref|NP_193919|]
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Pentatricopeptide repeat (PPR) superfamily protein [Arabidopsis thaliana]

Protein Classification

pentatricopeptide repeat-containing protein( domain architecture ID 13599395)

pentatricopeptide repeat (PPR)-containing protein may form anti-parallel alpha helices and bind single-stranded RNA in a sequence-specific and modular manner

CATH:  1.25.40.10
Gene Ontology:  GO:0003723
PubMed:  19004664|23635770|25882680|34065603|18031283|30809817
SCOP:  4001344

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 496-543 1.37e-12

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


:

Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 62.77  E-value: 1.37e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334186792  496 PNSSMYNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLIN-YC 543
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINgLC 49
PLN03218 super family cl33664
maturation of RBCL 1; Provisional
 494-774 3.45e-12

maturation of RBCL 1; Provisional


The actual alignment was detected with superfamily member PLN03218:

Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 70.29  E-value: 3.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  494 LAPNSSM--YNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLINYC---GEEATIAKYYKEMKQAGVEVNKHVY 568
Cdd:PLN03218  431 LIRNPTLstFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCaksGKVDAMFEVFHEMVNAGVEANVHTF 510

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  569 MSLVKAYASCGQFEKA---------KQVLMDLEVpakdhnelKSVLISALASNGNITEALSIYEEMKKLRCPVEPKAIL- 638
Cdd:PLN03218  511 GALIDGCARAGQVAKAfgaygimrsKNVKPDRVV--------FNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITv 582

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  639 -SLIENSDSNAELGTLVELTHELRdsKFWIDGFFKIIVFAVRNNRSSSILDLLEQTKNHLSKDDVGVEYWF--------- 708
Cdd:PLN03218  583 gALMKACANAGQVDRAKEVYQMIH--EYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFfsalvdvag 660

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334186792  709 -----EEVFKSIAETESSDVKVGLdlVSFMKeelelcpsrkcldfLLHACVNAKDKQSALLVWEEYQCAEL 774
Cdd:PLN03218  661 hagdlDKAFEILQDARKQGIKLGT--VSYSS--------------LMGACSNAKNWKKALELYEDIKSIKL 715
PPR_long super family cl38513
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 406-531 2.05e-07

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


The actual alignment was detected with superfamily member pfam17177:

Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 52.40  E-value: 2.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  406 SNEVVTALDIVENMCEAGLVISANILHSLL---------QAIEQILEFNLVQRIYSIMSNKSVKPNSETFRKSINLCIRI 476
Cdd:pfam17177  24 HADATGALALYDAAKAEGVRLAQYHYNVLLylcskaadaTDLKPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAK 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 334186792  477 KDFEGAYNMLGNLKNFNLAPNSSMYNSIMAGYFREKKVNSALKVLKEMKEADVKP 531
Cdd:pfam17177 104 GDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVEL 158
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 496-543 1.37e-12

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 62.77  E-value: 1.37e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334186792  496 PNSSMYNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLIN-YC 543
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINgLC 49
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 494-774 3.45e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 70.29  E-value: 3.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  494 LAPNSSM--YNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLINYC---GEEATIAKYYKEMKQAGVEVNKHVY 568
Cdd:PLN03218  431 LIRNPTLstFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCaksGKVDAMFEVFHEMVNAGVEANVHTF 510

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  569 MSLVKAYASCGQFEKA---------KQVLMDLEVpakdhnelKSVLISALASNGNITEALSIYEEMKKLRCPVEPKAIL- 638
Cdd:PLN03218  511 GALIDGCARAGQVAKAfgaygimrsKNVKPDRVV--------FNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITv 582

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  639 -SLIENSDSNAELGTLVELTHELRdsKFWIDGFFKIIVFAVRNNRSSSILDLLEQTKNHLSKDDVGVEYWF--------- 708
Cdd:PLN03218  583 gALMKACANAGQVDRAKEVYQMIH--EYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFfsalvdvag 660

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334186792  709 -----EEVFKSIAETESSDVKVGLdlVSFMKeelelcpsrkcldfLLHACVNAKDKQSALLVWEEYQCAEL 774
Cdd:PLN03218  661 hagdlDKAFEILQDARKQGIKLGT--VSYSS--------------LMGACSNAKNWKKALELYEDIKSIKL 715
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 406-531 2.05e-07

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 52.40  E-value: 2.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  406 SNEVVTALDIVENMCEAGLVISANILHSLL---------QAIEQILEFNLVQRIYSIMSNKSVKPNSETFRKSINLCIRI 476
Cdd:pfam17177  24 HADATGALALYDAAKAEGVRLAQYHYNVLLylcskaadaTDLKPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAK 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 334186792  477 KDFEGAYNMLGNLKNFNLAPNSSMYNSIMAGYFREKKVNSALKVLKEMKEADVKP 531
Cdd:pfam17177 104 GDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVEL 158
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 356-584 5.70e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 53.34  E-value: 5.70e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  356 TVSNLIfsyATCIPNSTVEDAIFKFNKLHEElDIVPSSTSYENLVSYLCGSNEVVTALDIVENMCEAGLVISANILHSLL 435
Cdd:PLN03218  581 TVGALM---KACANAGQVDRAKEVYQMIHEY-NIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALV 656

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  436 QAIEQILEFNLVQRIYSIMSNKSVKPNSETFRKSINLCIRIKDFEGAYNMLGNLKNFNLAPNSSMYNSIMAGYFREKKVN 515
Cdd:PLN03218  657 DVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLP 736

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334186792  516 SALKVLKEMKEADVKPDSVTFSYLINYCGEEATIA---KYYKEMKQAGVEVNKHVYMSLVkayASCGQ-FEKA 584
Cdd:PLN03218  737 KALEVLSEMKRLGLCPNTITYSILLVASERKDDADvglDLLSQAKEDGIKPNLVMCRCIT---GLCLRrFEKA 806
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 500-533 2.73e-06

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 44.37  E-value: 2.73e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334186792  500 MYNSIMAGYFREKKVNSALKVLKEMKEADVKPDS 533
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 603-630 1.98e-03

PPR repeat; 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 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 36.29  E-value: 1.98e-03
                          10        20
                  ....*....|....*....|....*...
gi 334186792  603 SVLISALASNGNITEALSIYEEMKKLRC 630
Cdd:pfam01535   4 NSLISGYCKNGKLEEALELFKEMKEKGI 31
 
Name Accession Description Interval E-value
PPR_2 pfam13041
PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is ...
 496-543 1.37e-12

PPR repeat family; This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.


Pssm-ID: 463778 [Multi-domain]  Cd Length: 50  Bit Score: 62.77  E-value: 1.37e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 334186792  496 PNSSMYNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLIN-YC 543
Cdd:pfam13041   1 PDVVTYNTLINGYCKKGKVEEAFKLFNEMKKRGVKPNVYTYTILINgLC 49
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 494-774 3.45e-12

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 70.29  E-value: 3.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  494 LAPNSSM--YNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLINYC---GEEATIAKYYKEMKQAGVEVNKHVY 568
Cdd:PLN03218  431 LIRNPTLstFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCaksGKVDAMFEVFHEMVNAGVEANVHTF 510

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  569 MSLVKAYASCGQFEKA---------KQVLMDLEVpakdhnelKSVLISALASNGNITEALSIYEEMKKLRCPVEPKAIL- 638
Cdd:PLN03218  511 GALIDGCARAGQVAKAfgaygimrsKNVKPDRVV--------FNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITv 582

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  639 -SLIENSDSNAELGTLVELTHELRdsKFWIDGFFKIIVFAVRNNRSSSILDLLEQTKNHLSKDDVGVEYWF--------- 708
Cdd:PLN03218  583 gALMKACANAGQVDRAKEVYQMIH--EYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFfsalvdvag 660

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334186792  709 -----EEVFKSIAETESSDVKVGLdlVSFMKeelelcpsrkcldfLLHACVNAKDKQSALLVWEEYQCAEL 774
Cdd:PLN03218  661 hagdlDKAFEILQDARKQGIKLGT--VSYSS--------------LMGACSNAKNWKKALELYEDIKSIKL 715
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 364-631 1.06e-11

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 68.75  E-value: 1.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  364 YATCIPNSTVEDAiFKFNKLHEEldivPSSTSYENLVSYLCGSNEVVTALDIVENMCEAGLVISANILHSLLQAIEQILE 443
Cdd:PLN03218  413 FKACKKQRAVKEA-FRFAKLIRN----PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGK 487

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  444 FNLVQRIYSIMSNKSVKPNSETFRKSINLCIRIKDFEGAYNMLGNLKNFNLAPNSSMYNSIMAGYFREKKVNSALKVLKE 523
Cdd:PLN03218  488 VDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAE 567

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  524 MK-EAD-VKPDSVTFSYLINYCG------------------------EEATIA--------------KYYKEMKQAGVEV 563
Cdd:PLN03218  568 MKaETHpIDPDHITVGALMKACAnagqvdrakevyqmiheynikgtpEVYTIAvnscsqkgdwdfalSIYDDMKKKGVKP 647

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  564 NKHVYMSLVKAYASCGQFEKAKQVLMDLE--------VP----------AKD-------HNELKSV-----------LIS 607
Cdd:PLN03218  648 DEVFFSALVDVAGHAGDLDKAFEILQDARkqgiklgtVSysslmgacsnAKNwkkalelYEDIKSIklrptvstmnaLIT 727

                         330       340
                  ....*....|....*....|....*
gi 334186792  608 ALASNGNITEALSIYEEMKKL-RCP 631
Cdd:PLN03218  728 ALCEGNQLPKALEVLSEMKRLgLCP 752
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 413-627 2.29e-11

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 67.59  E-value: 2.29e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  413 LDIVENMCEAGLVISANILHSLL-------QAIEQILEFNlvqriySIMSNksvkPNSETFRKSINLCIRIKDFEGAYNM 485
Cdd:PLN03218  390 IDLLEDMEKRGLLDMDKIYHAKFfkackkqRAVKEAFRFA------KLIRN----PTLSTFNMLMSVCASSQDIDGALRV 459

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  486 LGNLKNFNLAPNSSMYNSIMAGYFREKKVNSALKVLKEMKEA-----------------------------------DVK 530
Cdd:PLN03218  460 LRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAgveanvhtfgalidgcaragqvakafgaygimrskNVK 539

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  531 PDSVTFSYLINYCGEEATIAKYY---KEMKQAGVEVN-KHV-YMSLVKAYASCGQFEKAKQVL-MDLEVPAKDHNELKSV 604
Cdd:PLN03218  540 PDRVVFNALISACGQSGAVDRAFdvlAEMKAETHPIDpDHItVGALMKACANAGQVDRAKEVYqMIHEYNIKGTPEVYTI 619

                         250       260
                  ....*....|....*....|...
gi 334186792  605 LISALASNGNITEALSIYEEMKK 627
Cdd:PLN03218  620 AVNSCSQKGDWDFALSIYDDMKK 642
PPR_3 pfam13812
Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat ...
 485-546 7.62e-08

Pentatricopeptide repeat domain; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.


Pssm-ID: 316342 [Multi-domain]  Cd Length: 63  Bit Score: 49.66  E-value: 7.62e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334186792  485 MLGNLKNFNLAPNSSMYNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLINYCGEE 546
Cdd:pfam13812   2 ILREMVRDGIQLNVNTYTHLLHAYANVGNLKLALEIFERMKKKGIKPTLDTYNAILGVIGGR 63
PPR_long pfam17177
Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large ...
 406-531 2.05e-07

Pentacotripeptide-repeat region of PRORP; Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.


Pssm-ID: 407303 [Multi-domain]  Cd Length: 212  Bit Score: 52.40  E-value: 2.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  406 SNEVVTALDIVENMCEAGLVISANILHSLL---------QAIEQILEFNLVQRIYSIMSNKSVKPNSETFRKSINLCIRI 476
Cdd:pfam17177  24 HADATGALALYDAAKAEGVRLAQYHYNVLLylcskaadaTDLKPQLAADRGFEVFEAMKAQGVSPNEATYTAVARLAAAK 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 334186792  477 KDFEGAYNMLGNLKNFNLAPNSSMYNSIMAGYFREKKVNSALKVLKEMKEADVKP 531
Cdd:pfam17177 104 GDGDLAFDLVKEMEAAGVSPRLRSYSPALHAYCEAGDADKAYEVEEHMLAHGVEL 158
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 356-584 5.70e-07

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 53.34  E-value: 5.70e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  356 TVSNLIfsyATCIPNSTVEDAIFKFNKLHEElDIVPSSTSYENLVSYLCGSNEVVTALDIVENMCEAGLVISANILHSLL 435
Cdd:PLN03218  581 TVGALM---KACANAGQVDRAKEVYQMIHEY-NIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALV 656

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  436 QAIEQILEFNLVQRIYSIMSNKSVKPNSETFRKSINLCIRIKDFEGAYNMLGNLKNFNLAPNSSMYNSIMAGYFREKKVN 515
Cdd:PLN03218  657 DVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLP 736

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334186792  516 SALKVLKEMKEADVKPDSVTFSYLINYCGEEATIA---KYYKEMKQAGVEVNKHVYMSLVkayASCGQ-FEKA 584
Cdd:PLN03218  737 KALEVLSEMKRLGLCPNTITYSILLVASERKDDADvglDLLSQAKEDGIKPNLVMCRCIT---GLCLRrFEKA 806
PPR TIGR00756
pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR ...
 500-533 2.73e-06

pentatricopeptide repeat domain (PPR motif); This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.


Pssm-ID: 273253 [Multi-domain]  Cd Length: 35  Bit Score: 44.37  E-value: 2.73e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334186792  500 MYNSIMAGYFREKKVNSALKVLKEMKEADVKPDS 533
Cdd:TIGR00756   2 TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35
PLN03077 PLN03077
Protein ECB2; Provisional
 501-750 3.48e-06

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 51.00  E-value: 3.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 501 YNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLINYCGEEATIaKYYKEMK----QAGVEVNKHVYMSLVKAYA 576
Cdd:PLN03077 256 WNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDE-RLGREMHgyvvKTGFAVDVSVCNSLIQMYL 334

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 577 SCGQFEKAKQVLMDLEvpAKDHNELkSVLISALASNGNITEALSIYEEMKKLRCPVEPKAILSLIENSDSNAELGTLVEL 656
Cdd:PLN03077 335 SLGSWGEAEKVFSRME--TKDAVSW-TAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKL 411

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 657 tHELRDSKfwidGFFKIIVFAvrnnrsSSILDLLEQTKnHLSKDdvgveywfEEVFKSIAETessdvkvglDLVSFMKEE 736
Cdd:PLN03077 412 -HELAERK----GLISYVVVA------NALIEMYSKCK-CIDKA--------LEVFHNIPEK---------DVISWTSII 462

                        250
                 ....*....|....
gi 334186792 737 LELCPSRKCLDFLL 750
Cdd:PLN03077 463 AGLRLNNRCFEALI 476
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 456-694 2.92e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 47.56  E-value: 2.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 456 NKSVKPNSETFRKSINLCIRIKDFEGAYNMLGNLKNFNLAPNSSMYNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVT 535
Cdd:PLN03081 116 GCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTI 195

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 536 FSYLINYCGEEATIAkYYKEMKQAGVEVNKHVYMSLVKAYASCGQFEKAKQV-LMDLEVPAKDHNELKSVLISALASNGN 614
Cdd:PLN03081 196 IGGLVDAGNYREAFA-LFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLhCCVLKTGVVGDTFVSCALIDMYSKCGD 274

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 615 ITEALSIYEEMKKLRCPVEPKAILSLIENSDSNAELgtlvELTHELRDSKFWIDGF-FKIIVfavrnnRSSSILDLLEQT 693
Cdd:PLN03081 275 IEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEAL----CLYYEMRDSGVSIDQFtFSIMI------RIFSRLALLEHA 344


                 .
gi 334186792 694 K 694
Cdd:PLN03081 345 K 345
PLN03081 PLN03081
pentatricopeptide (PPR) repeat-containing protein; Provisional
 483-625 8.65e-05

pentatricopeptide (PPR) repeat-containing protein; Provisional


Pssm-ID: 215563 [Multi-domain]  Cd Length: 697  Bit Score: 46.02  E-value: 8.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 483 YNMLGNLKN----FNLAPNSSM--YNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLINYCGEEATI--AKY-Y 553
Cdd:PLN03081 269 YSKCGDIEDarcvFDGMPEKTTvaWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLehAKQaH 348

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334186792 554 KEMKQAGVEVNKHVYMSLVKAYASCGQFEKAKQVLMDLEvpakdHNELKS--VLISALASNGNITEALSIYEEM 625
Cdd:PLN03081 349 AGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP-----RKNLISwnALIAGYGNHGRGTKAVEMFERM 417
PPR_1 pfam12854
PPR repeat; This family matches additional variants of the PPR repeat that were not captured ...
 492-525 6.40e-04

PPR repeat; This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.


Pssm-ID: 403914 [Multi-domain]  Cd Length: 34  Bit Score: 37.71  E-value: 6.40e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 334186792  492 FNLAPNSSMYNSIMAGYFREKKVNSALKVLKEMK 525
Cdd:pfam12854   1 KGLKPDVVTYNTLINGLCRAGRVDEAFELLDEME 34
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 499-529 1.30e-03

PPR repeat; 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 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 37.06  E-value: 1.30e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 334186792  499 SMYNSIMAGYFREKKVNSALKVLKEMKEADV 529
Cdd:pfam01535   1 VTYNSLISGYCKNGKLEEALELFKEMKEKGI 31
PPR pfam01535
PPR repeat; This repeat has no known function. It is about 35 amino acids long and found in up ...
 603-630 1.98e-03

PPR repeat; 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 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR.


Pssm-ID: 366695 [Multi-domain]  Cd Length: 31  Bit Score: 36.29  E-value: 1.98e-03
                          10        20
                  ....*....|....*....|....*...
gi 334186792  603 SVLISALASNGNITEALSIYEEMKKLRC 630
Cdd:pfam01535   4 NSLISGYCKNGKLEEALELFKEMKEKGI 31
PLN03218 PLN03218
maturation of RBCL 1; Provisional
 391-540 2.30e-03

maturation of RBCL 1; Provisional


Pssm-ID: 215636 [Multi-domain]  Cd Length: 1060  Bit Score: 41.79  E-value: 2.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792  391 PSSTSYENLVSYLCGSNEVVTALDIVENMCEAGL---VISANILhslLQAIEQILEFNLVQRIYSIMSNKSVKPNSETFR 467
Cdd:PLN03218  717 PTVSTMNALITALCEGNQLPKALEVLSEMKRLGLcpnTITYSIL---LVASERKDDADVGLDLLSQAKEDGIKPNLVMCR 793

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334186792  468 KSINLCIRikDFEGAYNMLGNLKNFNLAPNSSmynsimagyfREKKVNSALKVLKEMKEADVKPDSVTFSYLI 540
Cdd:PLN03218  794 CITGLCLR--RFEKACALGEPVVSFDSGRPQI----------ENKWTSWALMVYRETISAGTLPTMEVLSQVL 854
PLN03077 PLN03077
Protein ECB2; Provisional
 392-634 2.41e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 41.76  E-value: 2.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 392 SSTSYENL-VSYLCGSNEVVTALDIVENMCEAGLVISANILHSLLQAIEQILEFNLVQRIYSIMSNKSVKPNSETFRKSI 470
Cdd:PLN03077  49 SSTHDSNSqLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAML 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 471 NLCIRIKDFEGAYNMLGNLKNFNLAPnssmYNSIMAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLINYCGEEATIA 550
Cdd:PLN03077 129 SMFVRFGELVHAWYVFGKMPERDLFS----WNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLA 204

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 551 KyykemkqaGVEVNKHVYM-----------SLVKAYASCGQFEKAKQVLMDLevPAKDHNELKSvLISALASNGNITEAL 619
Cdd:PLN03077 205 R--------GREVHAHVVRfgfeldvdvvnALITMYVKCGDVVSARLVFDRM--PRRDCISWNA-MISGYFENGECLEGL 273

                        250
                 ....*....|....*
gi 334186792 620 SIYEEMKKLRcpVEP 634
Cdd:PLN03077 274 ELFFTMRELS--VDP 286
PLN03077 PLN03077
Protein ECB2; Provisional
 382-584 2.67e-03

Protein ECB2; Provisional


Pssm-ID: 215561 [Multi-domain]  Cd Length: 857  Bit Score: 41.37  E-value: 2.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 382 KLHEeLDIVPSSTSY----ENLVSYLCGSNEVVTALDIVENMCEAGLVISANILHSLL---QAIEQILEFNlvqriYSIM 454
Cdd:PLN03077 410 KLHE-LAERKGLISYvvvaNALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRlnnRCFEALIFFR-----QMLL 483

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 455 SnksVKPNSETFRKSINLCIRI------KD-----------FEGAY-NMLGNL-----------KNFNL-APNSSMYNSI 504
Cdd:PLN03077 484 T---LKPNSVTLIAALSACARIgalmcgKEihahvlrtgigFDGFLpNALLDLyvrcgrmnyawNQFNShEKDVVSWNIL 560

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186792 505 MAGYFREKKVNSALKVLKEMKEADVKPDSVTFSYLINYCGEEATIAK---YYKEMKQA-GVEVNKHVYMSLVKAYASCGQ 580
Cdd:PLN03077 561 LTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQgleYFHSMEEKySITPNLKHYACVVDLLGRAGK 640


                 ....
gi 334186792 581 FEKA 584
Cdd:PLN03077 641 LTEA 644
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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