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: 2-Oct-2020
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:
Feature 1        ###    ##         #   # ##  #  #                                                
P52432        49 FRVGVVQMDe--DTLEFDMVGiDAAIANAFRRILLArvPTMAVEKVLVYNNTSIVQDEILAHRLGLIPILADprlfeyrn 126 house mouse
XP_002139766  64 IDIKINELTs--DYINFDLIGvDAAVANALRRILLVevPTVAIETVQIYQNSGVIQDEVLAHRLGLIPFNIDldlidfra 141 Cryptosporidium...
XP_001445184  31 LEINILSKTd--EKIVFEIINiDAPIANSLRRIMIAeiPTMAIHKVQVIQNTSVIPDEVLAHRLGLIPIIADplqfiekd 108 Paramecium tetr...
EEB01667      59 TSLKFLSVSp--ERVVFELKGvDAAIPNALRRILISevPTVAIETVQIWQNTGVVQDEVLAHRLGLIPFIVDptalnyrq 136 Toxoplasma gond...
XP_001738304   3 CQPRIIKISespEKVEFDAMGiDVSVANGLRRIMIAevPTMAIEMVVLEDNSSAIPDEMLCHRLGLIPILADprkfkfpk 82  Entamoeba dispa...
XP_001012875  44 IKIEVIRYDnknKELEFDLMGvDAPIANALRRIMIAevPTMAIHKVYIYQNTSIIPDEVLAHRLGLIPIYADprlfeekq 123 Tetrahymena the...
XP_001612274  34 VKIKFLKNTr--YHAIAEIEGlNVAIANAIRRILLAevPTLAIESVHIYQNTGVIQDEVLAHRLGLVPFDCNpdlipyrd 111 Babesia bovis T2Bo
CAQ40209      46 KNLEMKMHKneeNLLILEVKNlNVSIANALRRIMLAevPTIAIEKVNIFQNTGIIADEILCHRLGLIPFKFDadlinfke 125 Plasmodium know...
XP_001708454  29 NRLEYVIWKdecDTFSFDVINlSPVIANTIRRIILDevPTMAIDTVVVHENSSIIADEIFSHRLGLVPMNIDprlfeyhe 108 Giardia lamblia...
CAJ43894      38 GAGDGEPTRr-vETITSDMDNvSPPVANMFRRLMLTevPAFAFDRILIEHNDGVVPDELLAHRIGLVPLAGPvssmqyit 116 Trypanosoma bru...
Feature 1                                                                                        
P52432       127 qg----eeegteidtLQFRLQVRCTRNPNAakdssdp------nelyvnHKVYTRHMTWVPlgnqad--------vfpeg 188 house mouse
XP_002139766 142 e-----dqdlneknsVCFKLCVECNKYDIDdkng------------itsKAIYSKDLIWVPmsesqk-------qifekk 197 Cryptosporidium...
XP_001445184 109 d-----qeeynelnsIDFTLVAKCEKKPNSkhddpi-------eqqytnTTVHSSSLIWQPkgqqak--------lfaan 168 Paramecium tetr...
EEB01667     137 p-----nqevtdenaLRVSLHVKCTEQSLGphq--------------tsLPVYAKHIKWEPmspsqk-------eafaan 190 Toxoplasma gond...
XP_001738304  83 dr---hftdpteedtIVFTLDVTCTLDSAKnp---------------vnNKVYSSDLIWEPqgeqet--------tfadc 136 Entamoeba dispa...
XP_001012875 124 e-----edeyneknsLKFTLKIKCSKKEQYknyseadlenltpetylenAIVYSGDFKWVSqgeqnk--------kfeen 190 Tetrahymena the...
XP_001612274 112 n------edlsdknsVCFHLKVECKKESLAgr---------------tnLPVYAGDMKWVPlsdeqa-------elfkdn 163 Babesia bovis T2Bo
CAQ40209     126 e-----yekynhlncFCFKLHVKFTKKAGSse---------------tsQSIYSRDLKWCPineqqk-------lrfqkn 178 Plasmodium know...
XP_001708454 109 d-----gdkiherntVVFKLDVTAPATYSSsfnde----------epgwFYVYSRDIYWVPiggqkdwllkqevradmss 173 Giardia lamblia...
CAJ43894     117 dsasvgfdnldpervLLFELDVTAKRDVPT-------------------TSVYSGHLKWQPiakqeel-----aarsedd 172 Trypanosoma bru...
Feature 1                                       ##                                               
P52432       189 TIRPVHDDILIAQLRPGQEIDLMMHCVKGIGKDHAKFSPVATASYRLLPa-----------iTLLEPVEGEaaeeLSQCF 257 house mouse
XP_002139766 198 PPSVVYPDILITKLRPGQVIEAILYCEKGIGKTHAKWSPVSTATYRLLPef----------kFPEGYITGKdakeFVEVC 267 Cryptosporidium...
XP_001445184 169 PIRPVHSNIIIAKLRENQELNLRLICEKGVGKRHAKWSPVCTAFYKLMPs-----------iTIKNQLDAQrqekLASLC 237 Paramecium tetr...
EEB01667     191 PPRAVHPDILITKLRPGQEIELKAYLEKGVGKTHAKWSPVCTAVYRLEPe-----------iVFKESIQGEdasdLCSLC 259 Toxoplasma gond...
XP_001738304 137 PIKPVFDDILIAELQPHQHIKCKLFCCKGIGQDHAKFSPVCPATYRLMPk-----------iTVIKQNKKMsk-eIKNCC 204 Entamoeba dispa...
XP_001012875 191 PIRMVHDNIIVAKLRENQEIICEVICQKGIGKTHAKWSPVCTAYYRLMPe-----------iNINSDITGAkaqeLKERC 259 Tetrahymena the...
XP_001612274 164 PPKPIHKDILLTKLSPGQEIDLKAYLEKGIGKTHAKWSPVCTAVYRFKPdi---------tfSEDEPLTNDeveeLVQIC 234 Babesia bovis T2Bo
CAQ40209     179 PPKVVDDNILITKLANGQEIELICFLEKGIGKTHAKWSPVCTAVYKMYPsfsf-----ntceNFTKEEKND----LVNIC 249 Plasmodium know...
XP_001708454 174 LPAPLDPDILLAKLAPGQRIFCEIYCHKGIGRMHAKFQPVGTAWYKMKTqialdkdallqhpEVNGDVDKLvt-kLHKVC 252 Giardia lamblia...
CAJ43894     173 RVFLVHPDIVLTRLGPGQRLKLRAIAIKGIGAVHAKWTPVAACFYEMKQak---------agAEDSDGRASg--rGRSRS 241 Trypanosoma bru...
Feature 1                                                                                 #   #  
P52432       258 SPGVIEveev----qgkkVARVANa-RLDTFSREi--fRHEKLKKAVrl-----arVRDHYIFSVESTGvlPPDVLVSEA 325 house mouse
XP_002139766 268 PMNVFDied------itgKVYVKNp-RNCTTCRA----CIEKFPKKVei-----fkNKHHFIFSIESTGsiSPIQLVKTA 331 Cryptosporidium...
XP_001445184 238 PMKVFGvk--------gnQIKVVNp-RNCTTCRE----CVREANGFEkdve--lnkIDNHFIFSIESVGqyEAKDIMLQA 302 Paramecium tetr...
EEB01667     260 PMGVFDied------ttgEAYARYp-RNCTTCRA----CIERFPKEIel-----rkIKDHFIFSIESTGsvPAPLLFKMA 323 Toxoplasma gond...
XP_001738304 205 PLNVFDie--------dgELIVKNp-RNCKMCRE----CIREERSEYikl----grEENHYLFSVESTGiyPAKEIFSEA 267 Entamoeba dispa...
XP_001012875 260 PLKVYDvq--------nnKAIVSNe-RACTMCRE----CIREDEEFNsk-----ieLAKKKEHFIQSVGiyEPHEIVKEA 321 Tetrahymena the...
XP_001612274 235 PMGVFSad--------kgRITTIRp-YNCTSCRA----CLERFPKRVii-----kkLSNHFIFSVESTGaiPSGQLFLKA 296 Babesia bovis T2Bo
CAQ40209     250 PRNVFDved-------sdTLVAKNp-LNCSSCRV----CIEKYPKKIsf-----ekVKNHFIFTIESTGcfSSADIFRKA 312 Plasmodium know...
XP_001708454 253 PVNVFAdvtrqldiedfsVHHPDRt-EACTLCRE----CIAAFTDEQnqcgirlelVKTHLVFTIESCSwyRARDIYLEA 327 Giardia lamblia...
CAJ43894     242 GRGRVDa-----------NEEESNatRPRSASGNhshePHRETVNEVia-----krDTSSVRFTVESIGqlYAVDVFRQA 305 Trypanosoma bru...
Feature 1        ##  #     ##  
P52432       326 IKILMGKCRRFLDE 339 house mouse
XP_002139766 332 INILREKSHKINNS 345 Cryptosporidium muris RN66
XP_001445184 303 IEVFRSKVQLYIKE 316 Paramecium tetraurelia strain d4-2
EEB01667     324 IEILKEKALTFRQI 337 Toxoplasma gondii ME49
XP_001738304 268 VKIMKSKAEKLVTE 281 Entamoeba dispar SAW760
XP_001012875 322 IQILKQKASSFMLN 335 Tetrahymena thermophila SB210
XP_001612274 297 IGVLKEKSQKLKRR 310 Babesia bovis T2Bo
CAQ40209     313 LLILKDKVVSVKEV 326 Plasmodium knowlesi strain H
XP_001708454 328 LTVMQQKAALLKSS 341 Giardia lamblia ATCC 50803
CAJ43894     306 LILFAERIRDLAVR 319 Trypanosoma brucei brucei

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