6YMV,1S0V


Conserved Protein Domain Family
RPOL_N
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pfam14700: RPOL_N (This model is not part of the current CDD release)
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: 521376
Aligned: 167 rows
Threshold Bit Score: 128.096
Created: 16-Feb-2025
Updated: 28-Apr-2025
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: 
6YMV_A         326 RQKVLEN------RATEAARERWKHDFEEAKARGDisiekNLNVKLWKWYNEMLPLVKEEINHCRsllSEKLSDKkglnk 399  Saccharomyce...
EHB16924       390 QQLSVELasivhvESVEKTLSPTQETLEARK---------TLAALHTTWESELHSQLQKAKAHLA---KVTS-------- 449 
XP_003735468   469 QQLRVELastvcvKSVEKPVAQSKEVRRARE---------TLKVLRLQWEKALYEALQETKERLE-------REA----- 527 
XP_004778190   397 QQLRVEMattvavESVEQARVLTEEVLRARN---------TLQQLRAEWVEALCLGLRNLKASEV---CAAR-------- 456 
NP_001192480   391 QQLGVEMattvtvESVEKAPLLTEEVLQARK---------TLAALRAEWESVLSLELQETKESEA-------RAA----- 449 
XP_006101869   391 QQLSVEMativtvDSVEKAPSLTEEVLQARK---------TLQELRTRWEAELCLALQQTKAREA---QAAR-------- 450 
5_pfamImport     1 QQLRVELattvqvQSVDKAPPLTSEVLHARE---------TLRSLQAQWEAALCQELQEIKANLA---RTAH-------- 60  
12_pfamImport    1 QQLHVELttsvyiQSVEKAPSLTKEMLQARK---------TLKALRAQWEAALRRVLQETKASLA-------HQA----- 59  
NP_001100236   372 QQLHVELsssvsvQSVEEAPVMTKEVIEARK---------TLKALRSKWEVELLRVLRETKAKMG-------SQA----- 430 
XP_004910992   396 EQMAIESc----dTITIDSVEAIKPIAEGQKQARD-----LLDALRARWKKALLQAFRDSKKHLE------MKSR----- 455 

6YMV_A         400 vDTNRLGYGPYLTLIDPGKMCVITILELLKLNSTGG-ViegmrTARAVISVGKAIEMEFRSEQVLKsesqafrdvnkksp 478  Saccharomyce...
EHB16924       450 --YGHPTLYPFLCTVPEDELVQMLLQFLHTMPa----Fv------YVVHRLAMQTFQRHIVQQRRCrgqllaleqrymqy 517 
XP_003735468   528 -HTGLPSMFPFLCLLGEQEMVQMLLQALQALPAQGE-S-----FMGLARDLGARTFSRHEVQRQQFsgqvealkrhyrqy 600 
XP_004778190   457 --TGRPSVFPFLCVLPEKELAELLLQALQVLPPQGEsLl------SLAQQLGMRVFGRHAVRRQQRssrlqalqeryyqy 528 
NP_001192480   450 -AEGRPSLFPYLCLLSEKELVGLLLQTLQALPSHGE-S-----LFFLAHELGVRVLKRKRLRNQVEeleqryfeylhlla 522 
XP_006101869   451 --EGRPSLFPYLCLLSEGELTQLMLQTLQVLSQQGEsLl------SLAQELGMRIFNRHVVQRKQLndevqalqeryfky 522 
5_pfamImport    61 --GGRPTLYPHLCLLSERQMAQMLLQVLQVLPPQGEsLi------HLAHELGMRTFNRYVVQRKQRehqvqalqrrysey 132 
12_pfamImport   60 -HEGRPSLFPFLCLLSERELVRMLLQALYALPAQGE-S-----LVVVAKDLGLRTFNRHMVQQKRLnnqvqaleqryaqy 132 
NP_001100236   431 -YEGQPTLYPFLCLLSEGEFVSILMQALQVLPAQGE-P-----LFQLAQNLGLQVFNRHLVKQKQVtnhvqklgqqysqy 503 
XP_004910992   456 -ISPRVNLYPYLCLLGEDQYVDIMLQSLASIPPTGE-S-----FLVMSRDMGTKINNRYSIHKKLQeshinriqdlyrdy 528 

6YMV_A         479 efkk--------------lvqnaksvfrssqieqskILWPQSIRARIGSVLISMLIQVAKVSVQGVdpvt-kakvHGEAP 543  Saccharomyce...
EHB16924       518 lqllasdtq-----vaepclprqhwetlgppepappQVWPLMELLSLGKLLLEILVQSVQLPPSLAlpq----sssQPVP 588 
XP_003735468   601 lhllaadte-----vpepylprqywealgvseppqeQPWPLPVQVELGRLLAEILVQATKMPSNLAkpr----nsSRLVP 671 
XP_004778190   529 vrllasdtq-----veapqlprqywealgppeapheQPWPLSVLVQLGKKLAEMLVEAVRMPGSVAapq----gpgTLIP 599 
NP_001192480   523 sdtqva----------epclprqrwealgvpeappeQPWPVSVLVQLGKQLAEVLVRAVQMPSSLAaprg----pstlIP 588 
XP_006101869   523 lhllasdtq-----vvmsrlprqhwealgtteasqdQPWPLTVVVQLGKQLAEVLVQTVKMPSNLAqqq----dtqKLIP 593 
5_pfamImport   133 lrllacdtqv---dpprlprqhwemlggpggepppeQPWPLPVLLQLGKQLAEVLVRAVHMPRNLGapagkgagtePLIP 209 
12_pfamImport  133 lhllacdtq-----vaspclprqyweslgppeappqQPWPLPVLMQLGKQLAEMLVQAVHMPLGLAvpq----gscRPIP 203 
NP_001100236   504 lrllasdt------qvapclpreywdslgsletpaqQPWSVPVLLQLGKQLAELLVQAVQMPRSLAarh----gaQNFIP 573 
XP_004910992   529 cqllakngkvsgllpremweqleqkkyggaslmnldTIWPNSLLVQLGTHLVDLMVQEIKVPNDLLssr----ddPKLIP 604 

6YMV_A         544 AFAHGYQyhnGSKLGVLKIHKTLIRQlNGERLIASVQP--QLLPMLVEPKPWVNWRSGGYHYTQSTLLRTKDSP-EQVAY 620  Saccharomyce...
EHB16924       589 VLYHVYTfrgIRQIGFLRPHPAFIQL-LDDAAEPLMIFeaTDMPMLCPPLPWASSQSGGFLLSPTKLMRSVDGSlQHQNL 667 
XP_003735468   672 LLYHVYSfrnVYQIGFLKPHPAYVQL-LATAAEPTVTFeaVDVPMLCPPLPWTSPHTGAFLLNPTKLMRAVDGTmHHQRL 750 
XP_004778190   600 VLYHVYSfrsFRQIGILKPHPAFIEL-LATAAEHTLTFeaAEVPMLCPPLPWTSPHTGAFLLSPTKLMRSLEGTvQHQRL 678 
NP_001192480   589 VLYHVYSfrsFRQIGILKPHPAFTQL-QETAAERTLIFesTEVPMLCPPLPWTSPHSGAFLLSPTKMMRSLEGTqQHQLL 667 
XP_006101869   594 VLYHVYSfqsFRQIGILKPHPAFIQL-QETAAERTMTFesAEVPMLCPPLPWTSPHSGAFLLSPTKLMRSLEGTiQHQRL 672 
5_pfamImport   210 VLYHVYSfrsVRQIGILKPHPAFSQL-LAAAAEPTLTFeaAEVPMLCPPLPWTSPHSGAFLLSPAKLMRAVEGTmLHQQR 288 
12_pfamImport  204 VLYHVYSfrsYRQIGILKPHPAFTQL-LVAAADPTLTFetVDVPMLCPPLPWTSPHTGAFLLSPTKLMRAVEGTtQHQRL 282 
NP_001100236   574 VLYHVYSfrsYRQVGILKPHPAFTHL-LETAAEPTLTFetTEVPMLCPPLPWTSLHSGAYLLSSTKIMRATEGTtQHQRL 652 
XP_004910992   605 VLYHMYSfrsTKQIGLIKPHPIFSQI-QSDAGESCLTFesSVMPMLCPPVPWLSPRFGAYLLSPAKLMRCMEGA-VQHQL 682 

6YMV_A         621 LKAAsdngDIDRVYDGLNVLGR 642  Saccharomyces cerevisiae S288C
EHB16924       668 LDSWpp-tELHGALDTLTQLGN 688 
XP_003735468   751 LENCpp-aALHGALDTLTQLGN 771 
XP_004778190   679 LDSCpp-aDLHGALDALTQLGN 699 
NP_001192480   668 LERCpp-aELHGALDALTQLGN 688 
XP_006101869   673 LEGCpp-tELHGALDALTQLGN 693 
5_pfamImport   289 LEHCpp-aALHGAFDALTQLGN 309 
12_pfamImport  283 LERCpp-tNLHGALDTLTQLGN 303 
NP_001100236   653 LERCpp-aQLHGALDALTQLGN 673 
XP_004910992   683 LLEKsppgQLYPVLDSLNQLGM 704
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