1HQM,2GHO,1I6V,1L9U,1IW7,2O5I


Conserved Protein Domain Family
RNAP_beta'_C

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cd02655: RNAP_beta'_C 
Click on image for an interactive view with Cn3D
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain
Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Statistics
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PSSM-Id: 132721
View PSSM: cd02655
Aligned: 55 rows
Threshold Bit Score: 167.704
Threshold Setting Gi: 41017919
Created: 9-Oct-2007
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding site]
Evidence:
  • Comment:Bacterial RNAP beta' and beta subunits correspond to the Rpb1 (largest) and Rpb2 (second largest) subunits, respectively, of yeast RNAPII.
  • Structure:1HQM; Interface between the beta' (1HQM_D) and beta (1HQM_C) subunits of Thermus aquaticus RNAP; defined using 3.5A contacts
    View structure with Cn3D
  • Structure:2O5I; Interface between the beta' (2O5I_D) and beta (2O5I_C) subunits of Thermus thermophilus RNAP; defined at 3.5A contacts
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                #   #                                                                 
1HQM_D     954 RPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVg------------------------------------------- 990  Thermus aquaticus
Q2EEX0     323 KRVAIGEAIGIIAAQSIGEPGTQLTLRTFHTGGVGGfsganwisynspfdgfikfkkpvignilrswivmphytslnlvy 402  Helicosporidium ...
NP_852645  301 KHNNLGKNVGILSGQVIGEPGTQLTLRTFHTGGTFTlnlnkiknkdnfifnykyffninkyklcvkyhkikrlknnnkil 380  Eimeria tenella ...
CAA64574   305 YKYNLGQHIGVISSEAISEPSTQMVLRTFHASSILKdkfnfnkyliykiylyklninkifkliinfkkyinikfnliflm 384  malaria parasite...
NP_044750  909 EIVSLEESIGIIAAQSIGEPGTQLTMRTFHQGGTVLrganenrlyssynarvliynrkvvkginsitkinihrnskillf 988  Reclinomonas ame...
Q05FH9     835 KIVLIGVSVGIISAQSIGEPGTQLTMRTFHTGGVASyffysdnliisnsgfvkfkkckcvinkfgeviivslygefmifn 914  Candidatus Carso...
Q9PQV5    1016 KLIETGTAIGVIAAQSIGEPGTQLTMRTFHTGGVAGd------------------------------------------- 1052 Ureaplasma parvum
Q6F0L8     965 SLVKIGEPVGVIAAQSIGEPGTQLTMRTFHTGGVAGd------------------------------------------- 1001 Mesoplasma florum
Q98Q24    1104 RIVSIGEAVGITASQSIGEPGTQLTMRTFHSGGVAGv------------------------------------------- 1140 Mycoplasma pulmonis
P47582    1006 KLVELGTAVGVIAAQSIGEPGTQLTMRTFHTGGVSTe------------------------------------------- 1042 Mycoplasma genit...
Feature 1                                                                                      
1HQM_D         --------------------------------------------------------------------------------      Thermus aquaticus
Q2EEX0     403 kltpsfnelnltlfifdklknelynktlknegllfvregdfikkgqllfseininfknsnllktyipyysletgliispk 482  Helicosporidium ...
NP_852645  381 yfiylknnyfifksfyilfilkkykfnqilsinnrliysknniylsnllliylninniyqrkslininheqnytgeflyk 460  Eimeria tenella ...
CAA64574   385 nkilynynnilfeykyilqnqyikcnfiynsisknfkynlnniiikylnnvikyynysniqlliknihnkwilyniytyy 464  malaria parasite...
NP_044750  989 dlnysllisykipygatlyvddgsiiskgtllfdynsytipil------------------------------------- 1031 Reclinomonas ame...
Q05FH9     915 kiilekykfyygtkikfrngflikkntklinfndnnfy------------------------------------------ 952  Candidatus Carso...
Q9PQV5         --------------------------------------------------------------------------------      Ureaplasma parvum
Q6F0L8         --------------------------------------------------------------------------------      Mesoplasma florum
Q98Q24         --------------------------------------------------------------------------------      Mycoplasma pulmonis
P47582         --------------------------------------------------------------------------------      Mycoplasma genit...
Feature 1                                                                                      
1HQM_D         --------------------------------------------------------------------------------      Thermus aquaticus
Q2EEX0     483 lalnkylyplwiflfniiklnldslnskkftvyknysilekndlidlktilfeihfiqkskkfnlkkqeyllyqnlkmsl 562  Helicosporidium ...
NP_852645  461 nilqliiknkyykwiiinlnttilfnkyfpinyniikekiifiksknqryiklyliknknflysyrkyinklyhlkkifi 540  Eimeria tenella ...
CAA64574   465 lyyyhikfynlynkgiilnnnnnkynviyflinyfnlfsnyyykiynnnynfinsny----------------------- 521  malaria parasite...
NP_044750      --------------------------------------------------------------------------------      Reclinomonas ame...
Q05FH9         --------------------------------------------------------------------------------      Candidatus Carso...
Q9PQV5         --------------------------------------------------------------------------------      Ureaplasma parvum
Q6F0L8         --------------------------------------------------------------------------------      Mesoplasma florum
Q98Q24         --------------------------------------------------------------------------------      Mycoplasma pulmonis
P47582         --------------------------------------------------------------------------------      Mycoplasma genit...
Feature 1                                                                                      
1HQM_D         --------------------------------------------------------------------------------      Thermus aquaticus
Q2EEX0     563 ckshydystykklnvafqqnnqklnffynkklksslvsnninllwtsssysiniltksifniivfeylylslliknkyil 642  Helicosporidium ...
NP_852645  541 lniffsinyllliekylilkn-------------------------------tyilnynikyifniyntinlikckkkii 589  Eimeria tenella ...
CAA64574       --------------------------------------------------------------------------------      malaria parasite...
NP_044750      --------------------------------------------------------------------------------      Reclinomonas ame...
Q05FH9         --------------------------------------------------------------------------------      Candidatus Carso...
Q9PQV5         --------------------------------------------------------------------------------      Ureaplasma parvum
Q6F0L8         --------------------------------------------------------------------------------      Mesoplasma florum
Q98Q24         --------------------------------------------------------------------------------      Mycoplasma pulmonis
P47582         --------------------------------------------------------------------------------      Mycoplasma genit...
Feature 1                                                                                      
1HQM_D         --------------------------------------------------------------------------------      Thermus aquaticus
Q2EEX0     643 wilsknlkkkdkfhffkytstssskieifrlnskknslnirknklffysqnykknkvsnilfgnsiflkfplkkintffs 722  Helicosporidium ...
NP_852645  590 iwfkmflkvfytklkkknilkknniifpiklhinnniyifiyfkyfkinnitlsfnnliykesysiykkknklfnlinny 669  Eimeria tenella ...
CAA64574   522 ----------------yfkkmnfilknfnniqilnklfyvnnifiyykyekklfiylniinniiikkylnfykytynklf 585  malaria parasite...
NP_044750      --------------------------------------------------------------------------------      Reclinomonas ame...
Q05FH9         --------------------------------------------------------------------------------      Candidatus Carso...
Q9PQV5         --------------------------------------------------------------------------------      Ureaplasma parvum
Q6F0L8         --------------------------------------------------------------------------------      Mesoplasma florum
Q98Q24         --------------------------------------------------------------------------------      Mycoplasma pulmonis
P47582         --------------------------------------------------------------------------------      Mycoplasma genit...
Feature 1                                                                                      
1HQM_D         --------------------------------------------------------------------------------      Thermus aquaticus
Q2EEX0     723 qikqktinlkekktsnvegefigfqlknnikfwysispnslfsfkkdnkknrynfnfirknsnisgflvsntiktftlqk 802  Helicosporidium ...
NP_852645  670 ipklylidnlfyktiliqynfidinylfikniiipknivsqilhrqfinnnfnilllnnnkylinnflhiyyiyknyiyi 749  Eimeria tenella ...
CAA64574   586 fikkynnflylyeifkynwykylllnnkynlyiiynnyikylykynininlyfiknlfynnnnfihnhiiyknnyyiynn 665  malaria parasite...
NP_044750 1032 ------------------------------snykgnvffqeknqkissvkvrdsmsgivksnfnlginnfkrwflvnnsl 1081 Reclinomonas ame...
Q05FH9     953 -----------------------------------iysenigyvyfkkennivknyclednkfyyktlknfkitiinksi 997  Candidatus Carso...
Q9PQV5         --------------------------------------------------------------------------------      Ureaplasma parvum
Q6F0L8         --------------------------------------------------------------------------------      Mesoplasma florum
Q98Q24         --------------------------------------------------------------------------------      Mycoplasma pulmonis
P47582         --------------------------------------------------------------------------------      Mycoplasma genit...
Feature 1                                                                                      
1HQM_D     991 ------------------------------------tDITQGLPRVIELFEARRpkakaviseidgvvrieegedrlsvf 1034 Thermus aquaticus
Q2EEX0     803 giplifpsdtiyhkmekdfifknellcsfkslkpetqDIIQGIPRVEKLLEGRPlpfykpkvelykiwqfflknl----- 877  Helicosporidium ...
NP_852645  750 ttyytywknlfsnkyifnffrgiilnkkkyysnnsikDITSGLILIEIIFEAKIlpniyfipqkln-------------- 815  Eimeria tenella ...
CAA64574   666 nmnlyqynknilinnnllynklfynyinnniynlylnDITIGLQSINIIFENKNikdniffisnniyvifyikyynylnn 745  malaria parasite...
NP_044750 1082 kieninmsqdllnimensivkkgdvigrinisnkivqDITGGLSKISKLFECIQnqsclitpvegyikfnyepsvs---- 1157 Reclinomonas ame...
Q05FH9     998 kknyfipknfnivvycydyifpgeiiaklvsvtilksSIIGGLPRLSELFEARIpklkallseidgvckikfshlnyiit 1077 Candidatus Carso...
Q9PQV5    1053 ------------------------------------tNITQGFERIKQLFDCIQpqenekavisqvkgtveriekdsntn 1096 Ureaplasma parvum
Q6F0L8    1002 ------------------------------------aDITQGLPRIKELLDVTTqkgsvaiiaekagvvsdiinkngint 1045 Mesoplasma florum
Q98Q24    1141 ------------------------------------eDITGGFGRLTELIDAYRspwgrpaiiskvdgiiteiktpkdkn 1184 Mycoplasma pulmonis
P47582    1043 ------------------------------------nNLAQGFERLKQIFEVVTpkdfekavisevkgtvksittvqnaq 1086 Mycoplasma genit...
Feature 1                                                                                      
1HQM_D    1035 veseg----------fskeyklpkdarllvkdgdyveagqpltrgaIDPHQLLEAk------------------------ 1080 Thermus aquaticus
Q2EEX0     878 -------------------------gflkiknslfnlkkveskvylNNFKPNLNIgdicy-------------------- 912  Helicosporidium ...
NP_852645  816 -----------------------------------iltnifllyeeNTLNYLWNYslytfsynkkkllffteinsysnyi 860  Eimeria tenella ...
CAA64574   746 iiyiynicn--kyninhykyklnfysyifedissilysgyslhtefYSINKNLKYyfrfllksi---------------- 807  malaria parasite...
NP_044750 1158 -------------------------kfvlyvltkdektkkdllvriGTVHELDNLfvrqndyvyqgdll----------- 1201 Reclinomonas ame...
Q05FH9    1078 iiskfg---------fykeytlsclrklyinngdyvkigdilsdgkPDLNEIINLi------------------------ 1124 Candidatus Carso...
Q9PQV5    1097 gynvviky----nkdnyvnyptrsnavlrvktgdeiiagqkitegsIDVNDLLKYa------------------------ 1148 Ureaplasma parvum
Q6F0L8    1046 ivvteevn----gtqiekqyktmynavlrvnkgdqvkpgkkltegsINLHDLLEVa------------------------ 1097 Mesoplasma florum
Q98Q24    1185 tnlvyityldqddasqtevvsvpknrtlrvkvgdkivkgqkiidgpIILEELLEYg------------------------ 1240 Mycoplasma pulmonis
P47582    1087 evviksn-------vderiytipfsaqirvhvgdqvspgskitegsVDIKQLLRIa------------------------ 1135 Mycoplasma genit...
Feature 1                                                                                      
1HQM_D    1081 --------------------------------------------GPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQM 1116 Thermus aquaticus
Q2EEX0     913 ---------------------------------------layfhSKSNFGLDIASIISNVYLQEGVNISFKHIELIVREL 953  Helicosporidium ...
NP_852645  861 yenktsiltpnniiipgnysinilllklfshnlnfymqdqaiklSHIFIFNLIVESLLKQYFKNGINIPSIQFELIAKKM 940  Eimeria tenella ...
CAA64574   808 ------------------------------------niyqatksSYIYVYNILIESILKQYSYQNIYLPSIYFELIIKKM 851  malaria parasite...
NP_044750 1202 ------------------------------ssgivpireiaekiEFESSFYHLLEQIQSTYFENGVTINQKHIEVIISQM 1251 Reclinomonas ame...
Q05FH9    1125 --------------------------------------------SINYLLSYFVNEINSIYFPQNIYVNCKHIELILKQM 1160 Candidatus Carso...
Q9PQV5    1149 --------------------------------------------GIENVRHYIIKEVQKVYRMQGIEISDKYIEVIISQL 1184 Ureaplasma parvum
Q6F0L8    1098 --------------------------------------------GTTAVQNYILKEVQKVYRLQGIEISDKYIEIIVKQM 1133 Mesoplasma florum
Q98Q24    1241 --------------------------------------------GPRKVQSYLLKEIQKIYRMQGIAINDKYIEIIISQM 1276 Mycoplasma pulmonis
P47582    1136 --------------------------------------------GIQRVRQYMIVEIQKVYRIQGIDIADKYVEIIIRQL 1171 Mycoplasma genit...
Feature 1                                                                                      
1HQM_D    1117 LKYVEVTDPGdsp-lleGQVLEKWDVEALNerli-----------------aegkVPVAWKPLLMGVTKSALSTKSWLSA 1178 Thermus aquaticus
Q2EEX0     954 TSLVEIINPGdsg-fivKEKIHWLLIYNYNkrlk-----------------slnlKEISYMPIFLGMTEITKKKNSFGVA 1015 Helicosporidium ...
NP_852645  941 TSFVKINYSGdsa-lleNDIFDFNKLKILNyily-----------------tlgyKQILYSPVVLGITKSVLACSGFFAS 1002 Eimeria tenella ...
CAA64574   852 LSCIKIISNNfki-fkyNDIISLQLINIINysln-----------------lnkhYIYKYEPIILGITKSILANSGFLTN 913  malaria parasite...
NP_044750 1252 FFKITCMDLYldkdhfiNETKTSEIKEKINikykptrfnkdffchqsirllvmglLPIKGKISLGGISQIGVLGGSFLSS 1331 Reclinomonas ame...
Q05FH9    1161 TKKVKIIFSGess-cqqGDILFLEDAINENfstl-----------------vnsrRLSYYKRIVTGITKTSLESLSFFSA 1222 Candidatus Carso...
Q9PQV5    1185 TNKITITNPGdsg-lfvGETISINEFTEVAqnml-----------------vnkkKPPSAINQVFGLDHAPSKSGSFLSA 1246 Ureaplasma parvum
Q6F0L8    1134 LNKVKVIQSGesh-llqGEIVTQQKFKEVVtqci-----------------reglVPPVAKNQILGIKKAPLKSESWLSS 1195 Mesoplasma florum
Q98Q24    1277 LSKIEISEPGdsd-fiiGSLVNNLDFYNTNnell-----------------ekglEPAKGKVVIHGAKRIPLLSNSFLAA 1338 Mycoplasma pulmonis
P47582    1172 TNLLQVTDAGnsn-lfvGQLVHSHYLNELNksll-----------------lagkMPVIAINQVFGIDEAASKSNSFLSA 1233 Mycoplasma genit...
Feature 1                        #     #     #  ##   #  
1HQM_D    1179 ASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1219 Thermus aquaticus
Q2EEX0    1016 GSFQNLREIIIDHTFTRKTDYLLGLHENVLFNKIIPAGTGF 1056 Helicosporidium sp. ex Simulium jonesii
NP_852645 1003 ISFQEIIKFLKKLSIEHSIDWLSDLKSNIITTNLIKTGSGW 1043 Eimeria tenella strain Penn State
CAA64574   914 ISFQNTFKIISLNILNNKIDWLIDIKSKIILTDLLPVGNGW 954  malaria parasite P. falciparum
NP_044750 1332 ASFQKTSKVLTEAALWKGFDPLIGAQPNLFFGSLMPIGTGL 1372 Reclinomonas americana
Q05FH9    1223 ASFQETNKILVNSAIKNRTDYLLGLKENVLVGRLIPAGTGL 1263 Candidatus Carsonella ruddii PV
Q9PQV5    1247 ASFQDTKKILTDAAARSQKDMLIGLKENVILGNLIPAGTGL 1287 Ureaplasma parvum
Q6F0L8    1196 ASFQDTARVLTDAIIKGREDKLEGLKENIMLGNLIPAGTGL 1236 Mesoplasma florum
Q98Q24    1339 ASYQESAKILVNSSISSQQDFLVGVKENIILGKKIPAGTNS 1379 Mycoplasma pulmonis
P47582    1234 ASFQDTKKILTDAAVKNQVDYLLGLKENVIIGGKIPAGTGF 1274 Mycoplasma genitalium

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