Conserved Protein Domain Family
RNAP_I_II_AC40

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cd07032: RNAP_I_II_AC40 
AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III
The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC40 to RPB3 suggests a similar function. The AC40 subunit is likely to associate with the RPB11 counterpart, AC19, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III.
Statistics
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PSSM-Id: 132910
View PSSM: cd07032
Aligned: 39 rows
Threshold Bit Score: 277.553
Threshold Setting Gi: 88687066
Created: 19-Dec-2008
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
Feature 1:AC40 - AC19 heterodimer interface [polypeptide binding site]
Evidence:
  • Comment:based on the structures of the multi-subunit complexes of yeast RNAP II and archaeal RNAP
  • Comment:The AC40/AC19 heterodimer of eukaryotic RNAP I and II corresponds to the RPB3/RPB11 and D/L heterodimers of eukaryotic RNAP II and archaeal RNAP, respectively.
  • Comment:The yeast RNAP II RPB3/RPB11 (D/L) heterodimer, together with RPB10 (N) and RPB12 (P), anchors the two largest subunits, RPB1 (A'/A") and RPB2 (B), stabilizing their association.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1        ###    ##         #   # ##  #  #                                                
gi 18266895   49 FRVGVVQMDe--DTLEFDMVGiDAAIANAFRRILLArvPTMAVEKVLVYNNTSIVQDEILAHRLGLIPILADprlfeyrn 126
gi 209876648  64 IDIKINELTs--DYINFDLIGvDAAVANALRRILLVevPTVAIETVQIYQNSGVIQDEVLAHRLGLIPFNIDldlidfra 141
gi 145518624  31 LEINILSKTd--EKIVFEIINiDAPIANSLRRIMIAeiPTMAIHKVQVIQNTSVIPDEVLAHRLGLIPIIADplqfiekd 108
gi 211966471  59 TSLKFLSVSp--ERVVFELKGvDAAIPNALRRILISevPTVAIETVQIWQNTGVVQDEVLAHRLGLIPFIVDptalnyrq 136
gi 167387776   3 CQPRIIKISespEKVEFDAMGiDVSVANGLRRIMIAevPTMAIEMVVLEDNSSAIPDEMLCHRLGLIPILADprkfkfpk 82
gi 146164033  44 IKIEVIRYDnknKELEFDLMGvDAPIANALRRIMIAevPTMAIHKVYIYQNTSIIPDEVLAHRLGLIPIYADprlfeekq 123
gi 156089735  34 VKIKFLKNTr--YHAIAEIEGlNVAIANAIRRILLAevPTLAIESVHIYQNTGVIQDEVLAHRLGLVPFDCNpdlipyrd 111
gi 193809507  46 KNLEMKMHKneeNLLILEVKNlNVSIANALRRIMLAevPTIAIEKVNIFQNTGIIADEILCHRLGLIPFKFDadlinfke 125
gi 159116466  29 NRLEYVIWKdecDTFSFDVINlSPVIANTIRRIILDevPTMAIDTVVVHENSSIIADEIFSHRLGLVPMNIDprlfeyhe 108
gi 88687066   38 GAGDGEPTRr-vETITSDMDNvSPPVANMFRRLMLTevPAFAFDRILIEHNDGVVPDELLAHRIGLVPLAGPvssmqyit 116
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 18266895  127 qg----eeegteidtLQFRLQVRCTRNPNAakdssdp------nelyvnHKVYTRHMTWVPlgnqad--------vfpeg 188
gi 209876648 142 e-----dqdlneknsVCFKLCVECNKYDIDdkng------------itsKAIYSKDLIWVPmsesqk-------qifekk 197
gi 145518624 109 d-----qeeynelnsIDFTLVAKCEKKPNSkhddpi-------eqqytnTTVHSSSLIWQPkgqqak--------lfaan 168
gi 211966471 137 p-----nqevtdenaLRVSLHVKCTEQSLGphq--------------tsLPVYAKHIKWEPmspsqk-------eafaan 190
gi 167387776  83 dr---hftdpteedtIVFTLDVTCTLDSAKnp---------------vnNKVYSSDLIWEPqgeqet--------tfadc 136
gi 146164033 124 e-----edeyneknsLKFTLKIKCSKKEQYknyseadlenltpetylenAIVYSGDFKWVSqgeqnk--------kfeen 190
gi 156089735 112 n------edlsdknsVCFHLKVECKKESLAgr---------------tnLPVYAGDMKWVPlsdeqa-------elfkdn 163
gi 193809507 126 e-----yekynhlncFCFKLHVKFTKKAGSse---------------tsQSIYSRDLKWCPineqqk-------lrfqkn 178
gi 159116466 109 d-----gdkiherntVVFKLDVTAPATYSSsfnde----------epgwFYVYSRDIYWVPiggqkdwllkqevradmss 173
gi 88687066  117 dsasvgfdnldpervLLFELDVTAKRDVPT-------------------TSVYSGHLKWQPiakqeel-----aarsedd 172
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                       ##                                               
gi 18266895  189 TIRPVHDDILIAQLRPGQEIDLMMHCVKGIGKDHAKFSPVATASYRLLPa-----------iTLLEPVEGEaaeeLSQCF 257
gi 209876648 198 PPSVVYPDILITKLRPGQVIEAILYCEKGIGKTHAKWSPVSTATYRLLPef----------kFPEGYITGKdakeFVEVC 267
gi 145518624 169 PIRPVHSNIIIAKLRENQELNLRLICEKGVGKRHAKWSPVCTAFYKLMPs-----------iTIKNQLDAQrqekLASLC 237
gi 211966471 191 PPRAVHPDILITKLRPGQEIELKAYLEKGVGKTHAKWSPVCTAVYRLEPe-----------iVFKESIQGEdasdLCSLC 259
gi 167387776 137 PIKPVFDDILIAELQPHQHIKCKLFCCKGIGQDHAKFSPVCPATYRLMPk-----------iTVIKQNKKMsk-eIKNCC 204
gi 146164033 191 PIRMVHDNIIVAKLRENQEIICEVICQKGIGKTHAKWSPVCTAYYRLMPe-----------iNINSDITGAkaqeLKERC 259
gi 156089735 164 PPKPIHKDILLTKLSPGQEIDLKAYLEKGIGKTHAKWSPVCTAVYRFKPdi---------tfSEDEPLTNDeveeLVQIC 234
gi 193809507 179 PPKVVDDNILITKLANGQEIELICFLEKGIGKTHAKWSPVCTAVYKMYPsfsf-----ntceNFTKEEKND----LVNIC 249
gi 159116466 174 LPAPLDPDILLAKLAPGQRIFCEIYCHKGIGRMHAKFQPVGTAWYKMKTqialdkdallqhpEVNGDVDKLvt-kLHKVC 252
gi 88687066  173 RVFLVHPDIVLTRLGPGQRLKLRAIAIKGIGAVHAKWTPVAACFYEMKQak---------agAEDSDGRASg--rGRSRS 241
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                 #   #  
gi 18266895  258 SPGVIEveev----qgkkVARVANa-RLDTFSREi--fRHEKLKKAVrl-----arVRDHYIFSVESTGvlPPDVLVSEA 325
gi 209876648 268 PMNVFDied------itgKVYVKNp-RNCTTCRA----CIEKFPKKVei-----fkNKHHFIFSIESTGsiSPIQLVKTA 331
gi 145518624 238 PMKVFGvk--------gnQIKVVNp-RNCTTCRE----CVREANGFEkdve--lnkIDNHFIFSIESVGqyEAKDIMLQA 302
gi 211966471 260 PMGVFDied------ttgEAYARYp-RNCTTCRA----CIERFPKEIel-----rkIKDHFIFSIESTGsvPAPLLFKMA 323
gi 167387776 205 PLNVFDie--------dgELIVKNp-RNCKMCRE----CIREERSEYikl----grEENHYLFSVESTGiyPAKEIFSEA 267
gi 146164033 260 PLKVYDvq--------nnKAIVSNe-RACTMCRE----CIREDEEFNsk-----ieLAKKKEHFIQSVGiyEPHEIVKEA 321
gi 156089735 235 PMGVFSad--------kgRITTIRp-YNCTSCRA----CLERFPKRVii-----kkLSNHFIFSVESTGaiPSGQLFLKA 296
gi 193809507 250 PRNVFDved-------sdTLVAKNp-LNCSSCRV----CIEKYPKKIsf-----ekVKNHFIFTIESTGcfSSADIFRKA 312
gi 159116466 253 PVNVFAdvtrqldiedfsVHHPDRt-EACTLCRE----CIAAFTDEQnqcgirlelVKTHLVFTIESCSwyRARDIYLEA 327
gi 88687066  242 GRGRVDa-----------NEEESNatRPRSASGNhshePHRETVNEVia-----krDTSSVRFTVESIGqlYAVDVFRQA 305
                        330
                 ....*....|....
Feature 1        ##  #     ##  
gi 18266895  326 IKILMGKCRRFLDE 339
gi 209876648 332 INILREKSHKINNS 345
gi 145518624 303 IEVFRSKVQLYIKE 316
gi 211966471 324 IEILKEKALTFRQI 337
gi 167387776 268 VKIMKSKAEKLVTE 281
gi 146164033 322 IQILKQKASSFMLN 335
gi 156089735 297 IGVLKEKSQKLKRR 310
gi 193809507 313 LLILKDKVVSVKEV 326
gi 159116466 328 LTVMQQKAALLKSS 341
gi 88687066  306 LILFAERIRDLAVR 319

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