1CEZ,6YMV


Conserved Protein Domain Family
RPOL_N
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pfam14700: RPOL_N 
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DNA-directed RNA polymerase N-terminal
This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex.
Links
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Statistics
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PSSM-Id: 464270
Aligned: 171 rows
Threshold Bit Score: 121.95
Created: 25-Mar-2022
Updated: 17-Oct-2022
Structure
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Program:
Drawing:
Aligned Rows:
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PubMed ReferencesClick to see Conserved Features Help
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
1CEZ_A         35 EQLALEH------ESYEMGEARFRKMFERQLkagevadnaaakplittllpKMIARINDWFEEVKAKRGKRPTAFQ---- 104  Escherichia p...
XP_010600150  397 QQLRVELattvqvQSVDKAPPLTSEVLHARE--------------------TLRSLQAQWEAALCQELQEIKANLArtah 456 
EHB16924      390 QQLSVELasivhvESVEKTLSPTQETLEARK--------------------TLAALHTTWESELHSQLQKAKAHLAkvts 449 
XP_003735468  461 QQLRVELastvcvKSVEKPVAQSKEVRRARE--------------------TLKVLRLQWEKALYEALQETKERLEreah 520 
XP_013216952  385 QQLHVELttsvyiQSVEKAPSLTKEMLQARK--------------------TLKALRAQWEAALRRVLQETKASLAhqah 444 
EGV99464      370 QQLHVELsanvcvQSVEKAPVMTKEVIEARK--------------------TLKTLQGQWEAELLRVLQQTKATMAhqaq 429 
EDL89401      372 QQLHVELsssvsvQSVEEAPVMTKEVIEARK--------------------TLKALRSKWEVELLRVLRETKAKMGsqay 431 
XP_004778190  397 QQLRVEMattvavESVEQARVLTEEVLRARN--------------------TLQQLRAEWVEALCLGLRNLKASEVcaar 456 
NP_001192480  391 QQLGVEMattvtvESVEKAPLLTEEVLQARK--------------------TLAALRAEWESVLSLELQETKESEAraaa 450 
XP_006101869  391 QQLSVEMativtvDSVEKAPSLTEEVLQARK--------------------TLQELRTRWEAELCLALQQTKAREAqaar 450 

1CEZ_A        105 --------FLQEIKPEAVAYITIKTTLACLTSADnttVQAVASAIGRAIEDEARFGRIRDleakhfkknveeqlnkrvgh 176  Escherichia p...
XP_010600150  457 ggrptlypHLCLLSERQMAQMLLQVLQVLPPQGEsl--iHLAHELGMRTFNRYVVQRKQRehqvqalqrryseylrllac 534 
EHB16924      450 yghptlypFLCTVPEDELVQMLLQFLHTMPaf------vYVVHRLAMQTFQRHIVQQRRCrgqllaleqrymqylqllas 523 
XP_003735468  521 tglpsmfpFLCLLGEQEMVQMLLQALQALPAQGEs--FMGLARDLGARTFSRHEVQRQQFsgqvealkrhyrqylhllaa 598 
XP_013216952  445 egrpslfpFLCLLSERELVRMLLQALYALPAQGEs--LVVVAKDLGLRTFNRHMVQQKRLnnqvqaleqryaqylhllac 522 
EGV99464      430 egqptlypFLCLLSEGEFVSMLMQVLRLLPAQGEpl--lHLAHDLGLRVLNRHLVKQKQAtnhvqklgqhysqylrllas 507 
EDL89401      432 egqptlypFLCLLSEGEFVSILMQALQVLPAQGEpl--fQLAQNLGLQVFNRHLVKQKQVtnhvqklgqqysqylrllas 509 
XP_004778190  457 tgrpsvfpFLCVLPEKELAELLLQALQVLPPQGEsl--lSLAQQLGMRVFGRHAVRRQQRssrlqalqeryyqyvrllas 534 
NP_001192480  451 egrpslfpYLCLLSEKELVGLLLQTLQALPSHGEs--LFFLAHELGVRVLKRKRLRNQVEeleqryfeylhllasdtqva 528 
XP_006101869  451 egrpslfpYLCLLSEGELTQLMLQTLQVLSQQGEsl--lSLAQELGMRIFNRHVVQRKQLndevqalqeryfkylhllas 528 

1CEZ_A        177 vyk--kafmqvveadmlskgllggeawSSWHKEDSIHVGVRCIEMLIESTGMVSLHRqna------------------gv 236  Escherichia p...
XP_010600150  535 dtqvdpprlprqhwemlggpggepppeQPWPLPVLLQLGKQLAEVLVRAVHMPRNLGapagkgagteplipvlyhvysfr 614 
EHB16924      524 dtq--vaepclprqhwetlgppepappQVWPLMELLSLGKLLLEILVQSVQLPPSLAlpqsssqpvp----vlyhvytfr 597 
XP_003735468  599 dte--vpepylprqywealgvseppqeQPWPLPVQVELGRLLAEILVQATKMPSNLAkprnssrlvp----llyhvysfr 672 
XP_013216952  523 dtq--vaspclprqyweslgppeappqQPWPLPVLMQLGKQLAEMLVQAVHMPLGLAvpqgscrpip----vlyhvysfr 596 
EGV99464      508 dtq--veapclpreyweslgpletpmqQPWSLTVLLHLGKQLAEMLVQAVQMPRNLStpqasrhlip----vlyhvysfr 581 
EDL89401      510 dt---qvapclpreywdslgsletpaqQPWSVPVLLQLGKQLAELLVQAVQMPRSLAarhgaqnfip----vlyhvysfr 582 
XP_004778190  535 dtq--veapqlprqywealgppeapheQPWPLSVLVQLGKKLAEMLVEAVRMPGSVAapqgpgtlip----vlyhvysfr 608 
NP_001192480  529 -------epclprqrwealgvpeappeQPWPVSVLVQLGKQLAEVLVRAVQMPSSLAaprgpstlip----vlyhvysfr 597 
XP_006101869  529 dtq--vvmsrlprqhwealgtteasqdQPWPLTVVVQLGKQLAEVLVQTVKMPSNLAqqqdtqklip----vlyhvysfq 602 

1CEZ_A        237 vGQDSETIELAPEYAEAiaTRAGALAGISP--MFQPCVVPPKPWTGITGGGYWANGRrplALVRTHS---------KKAl 305  Escherichia p...
XP_010600150  615 sVRQIGILKPHPAFSQL--LAAAAEPTLTFeaAEVPMLCPPLPWTSPHSGAFLLSPA---KLMRAVEgtmlhqqrlEHCp 689 
EHB16924      598 gIRQIGFLRPHPAFIQL--LDDAAEPLMIFeaTDMPMLCPPLPWASSQSGGFLLSPT---KLMRSVDgslqhqnllDSWp 672 
XP_003735468  673 nVYQIGFLKPHPAYVQL--LATAAEPTVTFeaVDVPMLCPPLPWTSPHTGAFLLNPT---KLMRAVDgtmhhqrllENCp 747 
XP_013216952  597 sYRQIGILKPHPAFTQL--LVAAADPTLTFetVDVPMLCPPLPWTSPHTGAFLLSPT---KLMRAVEgttqhqrllERCp 671 
EGV99464      582 sYRQIGILKPHPAFSKL--LETAAEPTLILetTEVPMLCPPLPWTTPHTGAYLLSST---KLMRATEgttqhqhllERCa 656 
EDL89401      583 sYRQVGILKPHPAFTHL--LETAAEPTLTFetTEVPMLCPPLPWTSLHSGAYLLSST---KIMRATEgttqhqrllERCp 657 
XP_004778190  609 sFRQIGILKPHPAFIEL--LATAAEHTLTFeaAEVPMLCPPLPWTSPHTGAFLLSPT---KLMRSLEgtvqhqrllDSCp 683 
NP_001192480  598 sFRQIGILKPHPAFTQL--QETAAERTLIFesTEVPMLCPPLPWTSPHSGAFLLSPT---KMMRSLEgtqqhqlllERCp 672 
XP_006101869  603 sFRQIGILKPHPAFIQL--QETAAERTMTFesAEVPMLCPPLPWTSPHSGAFLLSPT---KLMRSLEgtiqhqrllEGCp 677 

1CEZ_A        306 mryedvYMPEVYKAINIAQN 325  Escherichia phage T7
XP_010600150  690 p----aALHGAFDALTQLGN 705 
EHB16924      673 p----tELHGALDTLTQLGN 688 
XP_003735468  748 p----aALHGALDTLTQLGN 763 
XP_013216952  672 p----tNLHGALDTLTQLGN 687 
EGV99464      657 p----aQLHGALDALTQLGN 672 
EDL89401      658 p----aQLHGALDALTQLGN 673 
XP_004778190  684 p----aDLHGALDALTQLGN 699 
NP_001192480  673 p----aELHGALDALTQLGN 688 
XP_006101869  678 p----tELHGALDALTQLGN 693
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