1I50,1HQM,2PMZ,2O5I,1I6H


Conserved Protein Domain Family
RNAP_largest_subunit_C

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cd00630: RNAP_largest_subunit_C 
Click on image for an interactive view with Cn3D
Largest subunit of RNA polymerase (RNAP), C-terminal domain
RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the 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, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Statistics
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PSSM-Id: 132719
View PSSM: cd00630
Aligned: 8 rows
Threshold Bit Score: 174.143
Threshold Setting Gi: 14278335
Created: 7-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 11 residues -Click on image for an interactive view with Cn3D
Feature 1:Rpb1 - Rpb2 interaction site [polypeptide binding site]
Evidence:
  • Comment:The two largest subunits, 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.
  • Structure:1I50; Interface between Rpb1 (1I50_A) and Rpb2 (1I50_B) subunits in Saccharomyces cerevisiae RNAP II; defined using 3.5A contacts
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1           #  #                                                                          
1I50_A       1061 GEMVGVLAAQSIGEPATQMTLNTFHFAGvask----kvtsGVPRLKEILNVAknmktpsltvylepghaadqeqaklirs 1136 baker's yeast
1HQM_D        959 GEAVGVVAAESIGEPGTQLTMRTFHTGGvavgt---ditqGLPRVIELFEARrpkakaviseidgvvrieegedrlsvfv 1035 Thermus aquat...
2PMZ_C         64 GEAIGIVAAQSVGEPGTQMTLRTFHFAGirel----nvtlGLPRLIEIVDAKkvpstpmmtiyltdeykrdrdkalevar 139  Sulfolobus so...
2O5I_D       1218 GEAVGIVAAQSIGEPGTQLTMRTFHTGGvagaa---ditqGLPRVIELFEARrpkakaviseidgvvrieeteeklsvfv 1294 Thermus therm...
1I6H_A       1061 GEMVGVLAAQSIGEPATQMTLNTFHFAGvask----kvtsGVPRLKEILNVAknmktpsltvylepghaadqeqaklirs 1136 baker's yeast
AAY89358      439 GEPVGVLAATALSQPAYESMLDAPHHSGwkirplelvqetLYPREKGDPKAVdrrailrlthcdcskssclerrvlrvqn 518  Sphagnum sp. ...
NP_191325    1155 GEPVGVLAAQSVGEPSTQMTLNTFHLAGrgem----nvtlGIPRLQEILMTAaaniktpimtcpllkgktkedanditdr 1230 thale cress
NP_001096178 1029 GSAVGALCAQSIGEPGTQMTLKTFHFAGvasm----nitlGVPRIKEIINASknistpiitahldidddadfarlvkgri 1104 western clawe...
Feature 1                                                                                         
1I50_A       1137 aiehttlksvtiaseiyydpdprstvipedeeiiqlhfslldeeaeqsfdqqspwllrleldraamndkdltmgqvgeri 1216 baker's yeast
1HQM_D       1036 eseg---------------------------------------------------------------------------- 1039 Thermus aquat...
2PMZ_C        140 kleytkienvvsstsidiasmsiilqldnemlkdkgvtvddvkkaigrlklgd--------------------------- 192  Sulfolobus so...
2O5I_D       1295 eseg---------------------------------------------------------------------------- 1298 Thermus therm...
1I6H_A       1137 aiehttlksvtiaseiyydpdprstvipedeeiiqlhfslldeeaeqsfdqqspwllrleldraamndkdltmgqvgeri 1216 baker's yeast
AAY89358      519 qlrriilktlaqtsiieywdatnerkagvngaalrlgspwlghihiskevlqqheltmtkivgklqrkfsilrpitkknp 598  Sphagnum sp. ...
NP_191325    1231 lrkitvadiiksmelsvvpytvyenevcsihklkinlykpehypkhtditeedweetmravflrkledaiethmkmlhri 1310 thale cress
NP_001096178 1105 ektllgeiseyieevflpddcfllvklslerirllrlevnaetvrysicmsklrvkpg---------------------- 1162 western clawe...
Feature 1                                                                                         
1I50_A       1217 kqt----------------------------------------------------------------------------- 1219 baker's yeast
1HQM_D            --------------------------------------------------------------------------------      Thermus aquat...
2PMZ_C            --------------------------------------------------------------------------------      Sulfolobus so...
2O5I_D            --------------------------------------------------------------------------------      Thermus therm...
1I6H_A       1217 kqt----------------------------------------------------------------------------- 1219 baker's yeast
AAY89358      599 lgqiffchsefcdvsrg--------------------------------------------------------------- 615  Sphagnum sp. ...
NP_191325    1311 rgihndvtgpiagnetdnddsvsgkqneddgdddgegtevddlgsdaqkqkkqetdemdyeensedetnepssisgvedp 1390 thale cress
NP_001096178      --------------------------------------------------------------------------------      western clawe...
Feature 1                                                                                         
1I50_A       1220 --------------------------------------------------fkndlfviwsedndekliircrvvrpksld 1249 baker's yeast
1HQM_D            --------------------------------------------------------------------------------      Thermus aquat...
2PMZ_C            --------------------------------------------------------------------------------      Sulfolobus so...
2O5I_D            --------------------------------------------------------------------------------      Thermus therm...
1I6H_A       1220 --------------------------------------------------fkndlfviwsedndekliircrvvrpksld 1249 baker's yeast
AAY89358      616 -------------------------------------lcihfspklpkkmqnqydddeyshsllelmkkmrdrilpalle 658  Sphagnum sp. ...
NP_191325    1391 emdsenedtevskedtpepqeesmepqkevkgvknvkeqskkkrrkfvraksdrhifvkgegekfevhfkfatddphill 1470 thale cress
NP_001096178 1163 ---------------------------------------------------------------------------diavh 1167 western clawe...
Feature 1                                                                                         
1I50_A       1250 aeteaeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvpgidptriyt 1329 baker's yeast
1HQM_D       1040 -------------------------------------------------fskeyklpkdarllvkdgdyveagqpltrga 1070 Thermus aquat...
2PMZ_C        193 -fmieesedstlninfanidsiaalfklrdkilntkikgikgikraivqkkgdeyiiltdgsnlsgvlsvkgvdvakvet 271  Sulfolobus so...
2O5I_D       1299 -------------------------------------------------fskeyklpkearllvkdgdyveagqpltrga 1329 Thermus therm...
1I6H_A       1250 aeteaeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvpgidptriyt 1329 baker's yeast
AAY89358      659 ctikgderlesvkivqedctwpswhpktagvvrpgeeelvlevvatsslhqkskrnmawnavmeacvpvmeevdwqrsmp 738  Sphagnum sp. ...
NP_191325    1471 aqiaqqtaqkvyiqnsgkierctvancgdpqviyhgdnpkerreisndekkaspalhasgvdfpalwefqdkldvrylys 1550 thale cress
NP_001096178 1168 geavlcvtprenskssmyyvlqslkedlpkvvvqgipevaravihideqsgkekykllvegdnlrsvmathgvkgsrtts 1247 western clawe...
Feature 1                                                                                         
1I50_A       1330 nSFIDIMEVlGIEAGRAALYKEVYNVIAsdgSYVNYRHMALLVDVMTTQg------------------------------ 1379 baker's yeast
1HQM_D       1071 iDPHQLLEAkGPEAVERYLVDEIQKVYRaqgVKLHDKHIEIVVRQMLKYvevtdpgdspllegqvlekwdvealnerlia 1150 Thermus aquat...
2PMZ_C        272 nNIREIEEVfGIEAAREIIIREISKVLAeqgLDVDIRHILLIADVMTRTg------------------------------ 321  Sulfolobus so...
2O5I_D       1330 iDPHQLLEAkGPEAVERYLVEEIQKVYRaqgVKLHDKHIEIVVRQMMKYvevtdpgdsrllegqvlekwdvealnerlia 1409 Thermus therm...
1I6H_A       1330 nSFIDIMEVlGIEAGRAALYKEVYNVIAsdgSYVNYRHMALLVDVMTTQg------------------------------ 1379 baker's yeast
AAY89358      739 ySIQEMKHAlGIEVAYQMVVQRVALALEetaPHTYREHIKLIGDTMTYSg------------------------------ 788  Sphagnum sp. ...
NP_191325    1551 nSIHDMLNIfGVEAARETIIREINHVFKsygISVSIRHLNLIADYMTFSg------------------------------ 1600 thale cress
NP_001096178 1248 nNTYEVEKTlGIEAARSTIINEIQYTMVnhgMSIDRRHVMLLADLMTYKg------------------------------ 1297 western clawe...
Feature 1                                                      #         ###     ## # #    #  
1I50_A       1380 ----------gLTSVTRhgfn-----rsntGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA 1440 baker's yeast
1HQM_D       1151 egkvpvawkplLMGVTKsal-------stkSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1219 Thermus aquaticus
2PMZ_C        322 ----------iVRQIGRhgvt-----geknSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGM 382  Sulfolobus solfat...
2O5I_D       1410 egktpvawkplLMGVTKsal-------stkSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478 Thermus thermophilus
1I6H_A       1380 ----------gLTSVTRhgfn-----rsntGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA 1440 baker's yeast
AAY89358      789 ----------dANGFTFsgfrdmiksahisAPFTEAAYQKPIRNFLDAAAKGAMDSLESVMTSCVWGREAPLGTGT 854  Sphagnum sp. JL-2005
NP_191325    1601 ----------gYRPMSRmggi-----aestSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGC 1661 thale cress
NP_001096178 1298 ----------eVLGITRfgla-----kmkeSVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGL 1358 western clawed frog

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