Conserved Protein Domain Family
RNAP_IV_NRPD1_C

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cd02737: RNAP_IV_NRPD1_C 
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain
Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Statistics
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PSSM-Id: 132724
View PSSM: cd02737
Aligned: 10 rows
Threshold Bit Score: 479.225
Threshold Setting Gi: 68300831
Created: 4-Oct-2007
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
Feature 1:putative Rpb1 (NRPD1) - Rpb2 interaction site [polypeptide binding site]
Evidence:
  • Comment:based on similarity to yeast RNAP II
  • Comment:The largest subunit of higher plant RNAP IV, NRPD1, corresponds to subunit Rpb1 of yeast RNAP II. The full subunit composition of RNAP IV is still unknown.
  • Comment:The two largest subunits of yeast RNAP II, Rpb1 and Rpb2, form distinct masses with a deep cleft between them. Each of the small subunits occurs in a single copy, arrayed around the periphery.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        #  #                                                                          
AAY89358   439 GEPVGVLAATALSQPAYESMLDAPHHSGwk-irPLELVQETLYPREKGDPKAVDRRAIL--RLTHCDCSKSsclerrVLR 515  Sphagnum sp. JL-...
AAY89357   433 GDAVGILAATAISQPAYQVMLEATQCLAsrkirPLELLQESLFPRSTSKLKESDRVSILrlHRCKSDGKYCee--rrVLK 510  liverwort
AAY89355   422 GEPVGFLAATAISQPAYQMLLESPNQLNdlafcPLELLQETIYSRKASVSKPNDLRVVLy-IKEVDGFSKEa----aAME 496  Ceratopteris tha...
CAH66955   868 VAPVGSWAACSISEAAYGALDHPVNSLEd---sPLMNLQEVLKCHKGTNSLDHTGLLFLskHLRKYRYGFEy----aSLE 940  Indian rice
AAY89360   567 GHPVGSLAACAISEAAYCALDQPVSALEs---sPLLNLKKILESGAGSRTGEKTASMFLskRLGRWAHGFEy----gALE 639  tomato
NP_176490  874 GEALGSLSACALSEAAYSALDQPISLLEt---sPLLNLKNVLECGSKKGQREQTMSLYLseYLSKKKHGFEy----gSLE 946  thale cress
CAO63655   787 GQPVGSISACAISEAAYSALDQPISLLEp---sPLLNLKRVLECGLRKSTADRTVSLFLskKLEKRKHGFEy----gALE 859  wine grape
EAZ21773   871 GEPVGVLAATAISNPAYKAVLDASQSNNt----SWERMKEILQTTSRYKNDMKDRKVILflNDCSCAKKFCke--kaAIA 944  Japanese rice
AAY89362   825 GEPVGVLAATAMSNPAYKAVLDSSPNSNs----SWELMKEVLLCKVNFQNTTNDRRVILylNECHCGKRFCqe--naACT 898  thale cress
EAZ14943   798 GDPVGILAATAVANAAYKAVLAPNQNNIi----SWDSMKEVLLTRASTKADANHRKVIL--YLNQCSCENEcm--erALT 869  Japanese rice
Feature 1                                                                                      
AAY89358   516 VQNQLRRIILKTLAQTSIIEYwdatnerkagvngaalrlgspwlghihi------------------------------- 564  Sphagnum sp. JL-...
AAY89357   511 LQDELQPVTMEILATETAIAYssdsseqweg------------------------------------------------- 541  liverwort
AAY89355   497 VSQSLQHVTLEMLLCSLSVKFvgnmqag---------------------------------------------------- 524  Ceratopteris tha...
CAH66955   941 VKDHLERVDFSDMVDTETMKIkrlglefivreiidqyn------------------------------------------ 978  Indian rice
AAY89360   640 VKGHLERLLLSEVVSTVMICFspe-------------------------------------------------------- 663  tomato
NP_176490  947 IKNHLEKLSFSEIVSTSMIIFsps-------------------------------------------------------- 970  thale cress
CAO63655   860 VKNHLEKLLFSDIVSTVMIVFspq-------------------------------------------------------- 883  wine grape
EAZ21773   945 VQGCLRRITLEDCATDICIEDgnwaapagfqhpvpppqckilpvpipipahgsvkfppvpipapehlkynihvvryqkqi 1024 Japanese rice
AAY89362   899 VRNKLNKVSLKDTAVEFLVEYrkqptiseifgidsclhghihlnktllqdwn---------------------------- 950  thale cress
EAZ14943   870 IRACLRRIKLEDCTTEISIKYqqqatqaahhlvghihldkkqlnqietimd----------------------------- 920  Japanese rice
Feature 1                                                                                      
AAY89358   565 ----------------------------skevlqqheltmtkivgklqrkfsilrpITKKNPLGQIFfchse-------- 608  Sphagnum sp. JL-...
AAY89357   542 -----------------------------------------------ldcaatelkQTEFFPWVGHVqldkmvltekkis 574  liverwort
AAY89355   525 --------------------------------------------------fwkgllPTKKSPWIVHMlldqtalsaynle 554  Ceratopteris tha...
CAH66955   979 ----------------------------------------tlrkqlnnaipsvsisNSKCSVGNECVk------------ 1006 Indian rice
AAY89360   664 -----------------------------------------------------trkSTHNCPWVCHFhidkenvktrrlk 690  tomato
NP_176490  971 -----------------------------------------------------sntKVPLSPWVCHFhisekvlkrkqls 997  thale cress
CAO63655   884 -----------------------------------------------------ngsKTHFSPWVCHFhvceeiakkrslk 910  wine grape
EAZ21773  1025 gldgtseaapalvghihldrahlerinistedilqkcqevsgkygkkkghlsnlfkNITFSTCDCLFtqklv-------- 1096 Japanese rice
AAY89362   951 --------------------------ismqdihqkcedvinslgqkkkkkatddfkRTSLSVSECCSfrdpc-------- 996  thale cress
EAZ14943   921 ---------------------------svlhkcqetfrnnikkkgsmreilktvtfISSTSLCDQHTddd---------- 963  Japanese rice
Feature 1                                                                                      
AAY89358   609 ------------------------------------------------fcdvsRGLCIHFspklpkkmq--nqydddeyS 638  Sphagnum sp. JL-...
AAY89357   575 qemildrlhskvkihksvsrkfrignivfcirdsctcdmniyqetvklrqkevVGPCLHFlltrstrgkvrsiktvkevS 654  liverwort
AAY89355   555 aeaiakkllntns--------------vhsfgalhfvargscdlscpgctrlsENPCLSFcls-------------taqS 607  Ceratopteris tha...
CAH66955  1007 ----------------------------------------------------nQTCCVSMvv---------------qvE 1019 Indian rice
AAY89360   691 lrsvldalnmryraa-----------ttkagndlpnlhitckdcsvaevqkekSEICITVsvv--------------etS 745  tomato
NP_176490  998 aesvvsslneqyksr----------nrelkldivdldiqntnhcssddqamkdDNVCITVtvv--------------eaS 1053 thale cress
CAO63655   911 phsiidalymkcnsa-----------raeskinlpdlqitskdcfvdmekedsDCFCITVsi---------------vnS 964  wine grape
EAZ21773  1097 ------------------------------------------------dgklpKLPCLQFfvsd-----------nmivS 1117 Japanese rice
AAY89362   997 ------------------------------------------------gskgsDMPCLTFsyn--------------atD 1014 thale cress
EAZ14943   964 --------------------------------------------------kkfQVSCLQFflpgs---------itkniS 984  Japanese rice
Feature 1                                                                                      
AAY89358   639 HSLLELMKKMRDRILPALLECTIKGDERLESVKIVQEDCtwpswhpkt---agvvrpgeeELVLEVVATSSlhqkskrnm 715  Sphagnum sp. JL-...
AAY89357   655 NETVELLEVLQNFIIPEILKTVVKGSEKLQSVNILWEDAtwsppvkseendsnvmksgrgELVLEVTVKELysqs--rgm 732  liverwort
AAY89355   608 PSIEEALSQIRDIIVPHIMKVSVRGDRRIKSVSILPSGIlseavpfgsq--ehyrersstEIALEVTIHGKlkstrqktn 685  Ceratopteris tha...
CAH66955  1020 INSMSQLDVIKERVIPSILATLLKGFLEFKNVKVQCQEDn--------------------ELVLKVGMSEHcks----gk 1075 Indian rice
AAY89360   746 KDPSSLLDTLRDVVIPFLLETVIKGFSAFKKVDILWKELpspsks---------srgptgELYLQVFMSEScdr----ik 812  tomato
NP_176490 1054 KHSVLELDAIRLVLIPFLLDSPVKGDQGIKKVNILWTDRpkapkrn--------gnhlagELYLKVTMYGDrgk----rn 1121 thale cress
CAO63655   965 KKSCIQLDTVRDLVIPFLLGAVVKGLLDVKKVDILWNDNpdsdvl----------ksssgRLYLRVYVSGDcgk----kn 1030 wine grape
EAZ21773  1118 ESVERAVSVLADSLCGVLLNTIIKGDPRIQEAKIVWVGSdatswvkn------tqkaskgEPAVEIIVEEEealh--igd 1189 Japanese rice
AAY89362  1015 PDLERTLDVLCNTVYPVLLEIVIKGDSRICSANIIWNSSdmttwirn------rhasrrgEWVLDVTVEKSavkq--sgd 1086 thale cress
EAZ14943   985 ESTERVIDFMTNAIFPIILDTVIKGDPRVEEANLVRIEPestfwvqs------sgaeqkgEAALEITVEEAaaae--sgn 1056 Japanese rice
Feature 1                                                                                      
AAY89358   716 aWNAVMEACVPVMEEVDWQRSMPYSIQEMKHALGIEVAYQMVVQRVALALEet-------------aPHTYREHIKLIGD 782  Sphagnum sp. JL-...
AAY89357   733 pWRTVQESCIQFVDYVDWQRSSPYSIQEIKSVLGVDAARDVLLQRLELAAG----------------NSIGNKHLKLVAD 796  liverwort
AAY89355   686 aWNVVLDLCGSVLHKINWLRSMPSGIQAIANVFGIEAAHNCIYHRLKSILSmf-------------dKTVYDHHVIVITE 752  Ceratopteris tha...
CAH66955  1076 fWATLQNACIPIMELIDWERSRPERVYDNFCSYGIDSAWKFFVESLRSTTDai-------------gRNIHRQHLLVVAD 1142 Indian rice
AAY89360   813 fWNALVDSCLQIRDLIDWERSYPDDVHDLTVAYGIDVAWEYFLCKLHSAVSet-------------gKKILPEHLVLAAD 879  tomato
NP_176490 1122 cWTALLETCLPIMDMIDWGRSHPDNIRQCCSVYGIDAGRSIFVANLESAVSdt-------------gKEILREHLLLVAD 1188 thale cress
CAO63655  1031 fWGVLMDACLQIMDMIDWERSHPDNIHDIFVVYGIDAGWKYFLNSLKSAISdi-------------gKTVLPEHLLLVAS 1097 wine grape
EAZ21773  1190 aWRTTMDACIPVLNLIDIRRSIPYGIQQVRELLGISCAFDQVVQRLSTTVRmv-------------aKDVLKDHLVLVAN 1256 Japanese rice
AAY89362  1087 aWRVVIDSCLSVLHLIDTKRSIPYSVKQVQELLGLSCAFEQAVQRLSASVRmv-------------sKGVLKEHIILLAN 1153 thale cress
EAZ14943  1057 aWGVAMNACIPVMDLIDTTRSMPYDIQQVRQVFGISSAFEKVTQVQLFPFLllaeiqylsksvgmitKSVLQEHLTTVAS 1136 Japanese rice
Feature 1                                               #         ###     ## # #    #        
AAY89358   783 TMTYSGDANGFTFSGFRDMIKSAHISAPFTEAAYQKPIRNFLDAAAKGAMDSLESVMTSCVWGREAPLGTGTKIELRW 860  Sphagnum sp. JL-2005
AAY89357   797 FMVYSGEVQGLTSYGYRDWMRSLKFSSPFTAGAFRAPIKHFLEAGRKGATERFSGVLASSVFGKKVPLGTGAVFDLNL 874  liverwort
AAY89355   753 LMTHSGNVIGLNAAGFREISNSLHISAPITQSLFQSSIKHIQTAALRGKCDDLSGTLAAICWGKLAPVGTGAKFDILW 830  Ceratopteris thali...
CAH66955  1143 CLSVSGQFHGLSSQGLKQQRTWLSISSPFSEACFSRPAHSFINAAKRDSVDNLSGTLDAIAWGKEPCTGSSGPFKILY 1220 Indian rice
AAY89360   880 SLTTTGEFVPLSAKGLTLQRKAAGVVSPFMQACFTNPGDSFVRAAKMGLSDDLQGSLESLAWGKTPSIGTGSSFDIMY 957  tomato
NP_176490 1189 SLSVTGEFVALNAKGWSKQRQVESTPAPFTQACFSSPSQCFLKAAKEGVRDDLQGSIDALAWGKVPGFGTGDQFEIII 1266 thale cress
CAO63655  1098 CLSATGEFVGLNAKGMARQKELTSISSPFMQGCFSSPGSCFIKAGKRAVADNLHGSLDALAWGKIPSVGSGGHFDILY 1175 wine grape
EAZ21773  1257 SMTFTGNLNGFNNAGYKATFRSLKVQVPFTESTLITPMKCFEKAAEKCHSDSLGCVVSSCSWGKHAASGTGSSFQILW 1334 Japanese rice
AAY89362  1154 NMTCSGTMLGFNSGGYKALTRSLNIKAPFTEATLIAPRKCFEKAAEKCHTDSLSTVVGSCSWGKRVDVGTGSQFELLW 1231 thale cress
EAZ14943  1137 SMTCTGDLHGFNNSGYKATCQSLKVQAPFMEATLSRSIQCFEKAAAKAYSDQLGNVVSACSWGNNAEIGTGSAFEILW 1214 Japanese rice

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