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: 17-Jan-2013
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:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1           #  #                                                                          
1I50_A       1061 GEMVGVLAAQSIGEPATQMTLNTFHFAGvask----kvtsGVPRLKEILNVAknmktpsltvylepghaadqeqaklirs 1136
1HQM_D        959 GEAVGVVAAESIGEPGTQLTMRTFHTGGvavgt---ditqGLPRVIELFEARrpkakaviseidgvvrieegedrlsvfv 1035
2PMZ_C         64 GEAIGIVAAQSVGEPGTQMTLRTFHFAGirel----nvtlGLPRLIEIVDAKkvpstpmmtiyltdeykrdrdkalevar 139
2O5I_D       1218 GEAVGIVAAQSIGEPGTQLTMRTFHTGGvagaa---ditqGLPRVIELFEARrpkakaviseidgvvrieeteeklsvfv 1294
1I6H_A       1061 GEMVGVLAAQSIGEPATQMTLNTFHFAGvask----kvtsGVPRLKEILNVAknmktpsltvylepghaadqeqaklirs 1136
gi 68300839   439 GEPVGVLAATALSQPAYESMLDAPHHSGwkirplelvqetLYPREKGDPKAVdrrailrlthcdcskssclerrvlrvqn 518
gi 15230368  1155 GEPVGVLAAQSVGEPSTQMTLNTFHLAGrgem----nvtlGIPRLQEILMTAaaniktpimtcpllkgktkedanditdr 1230
gi 156717272 1029 GSAVGALCAQSIGEPGTQMTLKTFHFAGvasm----nitlGVPRIKEIINASknistpiitahldidddadfarlvkgri 1104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1I50_A       1137 aiehttlksvtiaseiyydpdprstvipedeeiiqlhfslldeeaeqsfdqqspwllrleldraamndkdltmgqvgeri 1216
1HQM_D       1036 eseg---------------------------------------------------------------------------- 1039
2PMZ_C        140 kleytkienvvsstsidiasmsiilqldnemlkdkgvtvddvkkaigrlklgd--------------------------- 192
2O5I_D       1295 eseg---------------------------------------------------------------------------- 1298
1I6H_A       1137 aiehttlksvtiaseiyydpdprstvipedeeiiqlhfslldeeaeqsfdqqspwllrleldraamndkdltmgqvgeri 1216
gi 68300839   519 qlrriilktlaqtsiieywdatnerkagvngaalrlgspwlghihiskevlqqheltmtkivgklqrkfsilrpitkknp 598
gi 15230368  1231 lrkitvadiiksmelsvvpytvyenevcsihklkinlykpehypkhtditeedweetmravflrkledaiethmkmlhri 1310
gi 156717272 1105 ektllgeiseyieevflpddcfllvklslerirllrlevnaetvrysicmsklrvkpg---------------------- 1162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1I50_A       1217 kqt----------------------------------------------------------------------------- 1219
1HQM_D            --------------------------------------------------------------------------------
2PMZ_C            --------------------------------------------------------------------------------
2O5I_D            --------------------------------------------------------------------------------
1I6H_A       1217 kqt----------------------------------------------------------------------------- 1219
gi 68300839   599 lgqiffchsefcdvsrg--------------------------------------------------------------- 615
gi 15230368  1311 rgihndvtgpiagnetdnddsvsgkqneddgdddgegtevddlgsdaqkqkkqetdemdyeensedetnepssisgvedp 1390
gi 156717272      --------------------------------------------------------------------------------
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1I50_A       1220 --------------------------------------------------fkndlfviwsedndekliircrvvrpksld 1249
1HQM_D            --------------------------------------------------------------------------------
2PMZ_C            --------------------------------------------------------------------------------
2O5I_D            --------------------------------------------------------------------------------
1I6H_A       1220 --------------------------------------------------fkndlfviwsedndekliircrvvrpksld 1249
gi 68300839   616 -------------------------------------lcihfspklpkkmqnqydddeyshsllelmkkmrdrilpalle 658
gi 15230368  1391 emdsenedtevskedtpepqeesmepqkevkgvknvkeqskkkrrkfvraksdrhifvkgegekfevhfkfatddphill 1470
gi 156717272 1163 ---------------------------------------------------------------------------diavh 1167
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1I50_A       1250 aeteaeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvpgidptriyt 1329
1HQM_D       1040 -------------------------------------------------fskeyklpkdarllvkdgdyveagqpltrga 1070
2PMZ_C        193 -fmieesedstlninfanidsiaalfklrdkilntkikgikgikraivqkkgdeyiiltdgsnlsgvlsvkgvdvakvet 271
2O5I_D       1299 -------------------------------------------------fskeyklpkearllvkdgdyveagqpltrga 1329
1I6H_A       1250 aeteaeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvpgidptriyt 1329
gi 68300839   659 ctikgderlesvkivqedctwpswhpktagvvrpgeeelvlevvatsslhqkskrnmawnavmeacvpvmeevdwqrsmp 738
gi 15230368  1471 aqiaqqtaqkvyiqnsgkierctvancgdpqviyhgdnpkerreisndekkaspalhasgvdfpalwefqdkldvrylys 1550
gi 156717272 1168 geavlcvtprenskssmyyvlqslkedlpkvvvqgipevaravihideqsgkekykllvegdnlrsvmathgvkgsrtts 1247
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
1I50_A       1330 nSFIDIMEVlGIEAGRAALYKEVYNVIAsdgSYVNYRHMALLVDVMTTQg------------------------------ 1379
1HQM_D       1071 iDPHQLLEAkGPEAVERYLVDEIQKVYRaqgVKLHDKHIEIVVRQMLKYvevtdpgdspllegqvlekwdvealnerlia 1150
2PMZ_C        272 nNIREIEEVfGIEAAREIIIREISKVLAeqgLDVDIRHILLIADVMTRTg------------------------------ 321
2O5I_D       1330 iDPHQLLEAkGPEAVERYLVEEIQKVYRaqgVKLHDKHIEIVVRQMMKYvevtdpgdsrllegqvlekwdvealnerlia 1409
1I6H_A       1330 nSFIDIMEVlGIEAGRAALYKEVYNVIAsdgSYVNYRHMALLVDVMTTQg------------------------------ 1379
gi 68300839   739 ySIQEMKHAlGIEVAYQMVVQRVALALEetaPHTYREHIKLIGDTMTYSg------------------------------ 788
gi 15230368  1551 nSIHDMLNIfGVEAARETIIREINHVFKsygISVSIRHLNLIADYMTFSg------------------------------ 1600
gi 156717272 1248 nNTYEVEKTlGIEAARSTIINEIQYTMVnhgMSIDRRHVMLLADLMTYKg------------------------------ 1297
                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
Feature 1                                                      #         ###     ## # #    #  
1I50_A       1380 ----------gLTSVTRhgfn-----rsntGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA 1440
1HQM_D       1151 egkvpvawkplLMGVTKsal-------stkSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1219
2PMZ_C        322 ----------iVRQIGRhgvt-----geknSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGM 382
2O5I_D       1410 egktpvawkplLMGVTKsal-------stkSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
1I6H_A       1380 ----------gLTSVTRhgfn-----rsntGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA 1440
gi 68300839   789 ----------dANGFTFsgfrdmiksahisAPFTEAAYQKPIRNFLDAAAKGAMDSLESVMTSCVWGREAPLGTGT 854
gi 15230368  1601 ----------gYRPMSRmggi-----aestSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGC 1661
gi 156717272 1298 ----------eVLGITRfgla-----kmkeSVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGL 1358

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