Conserved Protein Domain Family
RNAP_III_Rpc1_C

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cd02736: RNAP_III_Rpc1_C 
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain
Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Statistics
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PSSM-Id: 132723
View PSSM: cd02736
Aligned: 26 rows
Threshold Bit Score: 403.522
Threshold Setting Gi: 162606212
Created: 5-Oct-2007
Updated: 17-Jan-2013
Structure
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Aligned Rows:
  next features
Feature 1:Rpb1 (Rpc1) - Rpb2 (Rpc2) interaction site [polypeptide binding site]
Evidence:
  • Comment:based on similarity to yeast RNAP II
  • Comment:The two largest subunits of eukaryotic RNAP III, Rpc1 and Rpc2, correspond to subunits Rpb1 and Rpb2, respectively, of yeast RNAP II.
  • 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:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    #  #                                                                 
gi 156717272 1020 KYMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAHLdi--------- 1090
gi 46229106  1452 KYMKAITEPGEAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAATKILTPIIEAKLen--------- 1522
gi 133352    1282 KYIRLNLEPGSPCGAVAAQSVGEPSTQMTLKSFHHAGLASMNITQGVPRLKEIVDGVVKISTPITTVELhvdvdkee--- 1358
gi 118346269 1035 RYPQMLVEPGEAVGAVGATSISEPATQMTLKSFHFAGVASMNITQGVPRMKEIIDAAKKISTPIIDVKLlpq-------- 1106
gi 162606212  947 TFKLVIIDPGTGVGCISAQSLGEPGTQMTLQTFHSAGTGSQNITSGIPRINEILSNSKNTKFPLISYDInf--------- 1017
gi 71665443  1139 KYILKACEPGTPCGAIAAQSVGEPSTQMTLRTFHFAGVASMSITQGVPRLVEIINANRNIATPVVTAPVrrhrrgkslsi 1218
gi 74830400   971 RFLTMVMAPGTSVGPITSQSIGEPATQMTLKTFHSAGVAGMSITQGVPRLNEIINASKEIKTPQINVKLinrqvmdhakq 1050
gi 71029280  1270 DYQKSLCEPGEAIGALGSQSIGEPATQMTLKTFHFAGVASMNVTLGVPRIQEIINATSLIATPIIEVPLed--------- 1340
gi 154417868  994 RCEKSMAEPGMTVGAVAGQSIGEPATQMTLRSFHFAGVASMNVTLGVPRIEEVMNAVSEIKTPIITANLls--------- 1064
gi 67476290  1024 KGLRSVCEAGTPVGALAGQSMGEPSTQMVLKTFHFAGVASMNIALGVPRIKEIINASKKIQTPIVTAKLvn--------- 1094
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 156717272 1091 ----------------ddDADFARLVKGRIEKTLLGEISEYIEEVFLPDDCFLLVKLSLERIRLLRLevnaetvrysicm 1154
gi 46229106  1523 ----------------dsDFNYAQIVKGSIVKTLLNEVVSDIEELYSPNGVFININLNEETIKGHYLdinaytvrdsivs 1586
gi 133352    1359 ----------laatvtekYLEKARMMKNIIECTYLGQISASIIECYSQSVCHIEVNLDMKIIADMGLagiitvetvvasi 1428
gi 118346269 1107 ----------------fqSEHSYRSIRLQIEKTYLGEISNFYQEVYSPKDCHLYIEYNKKKLEQFRLygleiplssikkg 1170
gi 162606212 1018 ----------------feFNKKKSRLKFFLKKIKIGFLINSIEIFLHRGFVSVKIHFIKKIYEYLDQskiyyfiikkfhd 1081
gi 71665443  1219 kqe--vvgesceedsqeeFEKRVRRVKSQVERVLLKEVASEIVEVCTSTEFYLRVHLNMSLIAKLWLpinaitvrqrila 1296
gi 74830400  1051 faksgdpqyeyahravihSAQQAQDVNIQIEQTKLMQILKKMDEIYTADNCYIELELDCHCLARLKLefvtpkyvcalil 1130
gi 71029280  1341 ----------------ntDYDFALKVKSKIEKTTLGQICLNIKQLYTPQMSKLLFTLNRDLIEQLHIqvnadkvrdiiid 1404
gi 154417868 1065 ----------------qrDEIAARIVKGIIDRVTLGQVCKHIEYNQNEKSCYIDIELDAEIIREAKLnitsetvrrsivn 1128
gi 67476290  1095 ----------------sqDVTSARIVKGRIEATRLKEIAKSVKIVFKPAEAYISVKLDFETIKQLELectiekvqdvlln 1158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 156717272 1155 sklrvk-----------------------------pgdiavhgeavlcvtprenSKSSMYYVLQSLKeDLPKVVVQGIPE 1205
gi 46229106  1587 hgpiskiklklediqvldlwklsiligggisqigsssnningtgnvntlntgigNTMNVYFQTQLLKkGLQNVVVSGIPG 1666
gi 133352    1429 lhndkakklvg--------------------qdqssgsvsihsatrfsvrpltqSRDDLLFDIQSLKlLLPMIPVSGIST 1488
gi 118346269 1171 ileiakdike---------------------dqiiavkdqdlkpvgikinpgndVKKNVFFKIQNWKkILPGAVVSGMKD 1229
gi 162606212 1082 ntkiikkstv----------------------fickkkknvvlqfhkndfkiddFNLNFINLYNFFRiHFGDIVLTGFYE 1139
gi 71665443  1297 aaarpmsplr----------------------llreecvevvsldtlavrpyflEAHRVHFNLRHVLaLLPDVVVGGIAG 1354
gi 74830400  1131 kelklspd--------------------------dvkydlkiiritvkksskkkQSENLLFLIKELQrKLLRLHIYGCAN 1184
gi 71029280  1405 sgclgkv---------------------------kihkscvysigkwqicielpSNQQHFFQQNSLIsGLTQLVVAGSKS 1457
gi 154417868 1129 tpkigvk----------------------------dentanngdynvrvfmqgaNPKAFSFIMQQLMlKLPDVVVSGVPG 1180
gi 67476290  1159 yrglkl-----------------------------kdnqviirnkqklrvyvdkSSTSLLFALNSLRnQLLEVIVCGIEN 1209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 156717272 1206 VARAVIHIdeqs--------gkekYKLLVEGDNLRSVMATHGVKGSRTTSNNTYEVEKTLGIEAARSTIINEIQYTMVnh 1277
gi 46229106  1667 IKRSVIRQddkedpi--tgekrkcYSLAVEGYGLLKLMGINGIIGTTTVSNHVMEVREVLGIEAARKVIIQEVQKCMDay 1744
gi 133352    1489 CSRAVINEykefcqgatssapltkYNLLVEGIGLQNILNVSGIDFTRTLSNNIVEVANTLGIEAAVATISNEIKACMDsh 1568
gi 118346269 1230 VKRVSISKdkkkgd-----kneykFDLFVEGNSFKQVLQLDEVDFANTLSVDIFEVLQILGVEAARKTIINEITKTIKsh 1304
gi 162606212 1140 SSKINCNFlf------------nnLEIKISDNRFDILLNIPGIIFRKLYCNNINSIYNFLGIEASRELIVLEITNTFKsh 1207
gi 71665443  1355 INRAMISSn--------------gAEVLAEGAELRAVMNLPEVESTRVVCNHVAVVERVLGIEAARQVIVNEIQGILKay 1420
gi 74830400  1185 IKQTVIQVtdkddk----envkgeARLFASGIGFKEILRLDNIDWKRTVSNHIMEIQSALGIEAARQSIVNEVYTTMQsh 1260
gi 71029280  1458 VKRAVIKRestp--------qgpnYQIAVEGYGLQEVMGCYGVMSSAVKSNHVAEVAKVLGIEAARSVIISEIQRCMDay 1529
gi 154417868 1181 VERVHVGKen------------gcFKLFVEGNPFLKVLNTPGIDPKRTVSNHVLDVEKVLGVEAARSVIISEITNVMKny 1248
gi 67476290  1210 TGRAVINKnk------------gsFELLVEGSELLKVMGTPGVIGEETTSNHIAVVEKVLGIEAARSTIISEIKNVMDay 1277
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                            #         ###     ## # #    #
gi 156717272 1278 GMSIDRRHVMLLADLMTYKGEVLGITRFGLAKMk-eSVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGT 1356
gi 46229106  1745 SMDIDLRHIQLLADIMTFRGDVLGISRFGIQKMr-tSTLMLASFEETNEHLFEAAFQNRVDPVFGVSECVIMGKPIKIGT 1823
gi 133352    1569 GMAVDMRHIRLLADIMCFRGRVLGFTRFGLTKMkadSVIMLASFEKTGEHLFNAALGNKVDEANGVTESIILGKPMSMGT 1648
gi 118346269 1305 SLNVDRRHLILVADVLTSKGRLHGSTRQGINSMk-dSTLMLASFEKTTEILYNAALQGRKDTLEGVSERIIIGQNIPMGT 1383
gi 162606212 1208 GIFSDNRHVYLLADYMTFNGFIIGINREGLTCNk-eSVFLLASFEKTMENLFNASLNHTKSKYIGVSDAIIFGNSIPIGT 1286
gi 71665443  1421 SLSIDIRHIYLLADLMTQRGVVLGITRYGIQKMn-fNVLTMASFERTTDHLYNAAATQRVDENLSVSESIIIGKPVPLGT 1499
gi 74830400  1261 SISIDIRHILLLAELMTFKGRILGFTRQGIDQLk-nSALMLASFEKTMDVFFNAAIQGKQDSMNGASQRVIIGQNVPQGT 1339
gi 71029280  1530 SIDIDCRYMKLLGDVMTFRGEVVGINRFGIQKMr-sSALMLASFEETNDHLLEAALHHRRDPIKGVSECIIMGKPISLGT 1608
gi 154417868 1249 SLNIDRRHLMLLSDLMTIRGKVLGVTRHGLAKTs-vSSLKLASFETTQEHLFNAAFHNVDEVANGVSASVILGNFAPIGS 1327
gi 67476290  1278 GLSIDVRHLLLLSDLMTFKGVILGITRYGISKMk-dSVFTFASFERTNDHLFDAAVHSRKDEIKGVSESIIVGNQVGLGT 1356

                  ...
Feature 1            
gi 156717272 1357 GLF 1359
gi 46229106  1824 GSF 1826
gi 133352    1649 GSF 1651
gi 118346269 1384 GTF 1386
gi 162606212 1287 GLI 1289
gi 71665443  1500 TSF 1502
gi 74830400  1340 GMF 1342
gi 71029280  1609 GSF 1611
gi 154417868 1328 GMI 1330
gi 67476290  1357 GLM 1359

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