1TLH,1TTY,1L9U,1L9Z,1IW7,2H27,1OR7,1RP3,1RP3,2O8X,2Z2S,2Q1Z


Conserved Protein Domain Family
Sigma70_r4

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cd06171: Sigma70_r4 
Click on image for an interactive view with Cn3D
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).
Statistics
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PSSM-Id: 100119
View PSSM: cd06171
Aligned: 72 rows
Threshold Bit Score: 43.6322
Threshold Setting Gi: 122921482
Created: 8-Jan-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA binding
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:DNA binding residues [nucleic acid binding site]
Evidence:
  • Comment:based on the binding of E. coli sigmaE SR4 and T. aquaticus sigmaA SR4 to their -35 elements. These proteins use distinct mechanisms. E. coli sigmaE SR4 binds 4 A further into the major groove than the latter, making more extensive contacts. It also recognizes a different -35 consensus sequence than that of Thermus aquaticus sigmaA.
  • Structure:2H27_A, Escherichia coli sigmaE SR4 bound to its -35 element 7-base-pair consensus GGAACTT DNA, contacts at 3.5 A.
    View structure with Cn3D
  • Structure:1L9Z_H, Thermus aquaticus RNA polymerase holoenzyme/ FORK-Junction promoter complex, showing sigmaA bound with a promoter DNA fragment, contacts at 3.5A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*....
Feature 1                 #         #         ##         # ## ### ## #    
1TLH_B       9 RAATHDVLAGLTAREAKVLRMRfgidmntDYTLEEVGKQFdvTRERIRQIEAKALRKLR 67
2H27_A      10 RQIVFRTIESLPEDLRMAITLRel----dGLSYEEIAAIMdcPVGTVRSRIFRAREAID 64
gi 585930  170 KQLLLFALKKLNEREKRIVELRygltgvgEKTQKEVADMLgiSQSYISRLEKRIIKRLK 228
gi 133472  174 KKLLKKALEQLNEREKQIMELRfglvgeeEKTQKDVADMMgiSQSYISRLEKRIIKRLR 232
gi 133478  219 LEKVKQYIDILDDREKEVIVGRfgldlkkEKTQREIAKELgiSRSYVSRIEKRALMKMF 277
gi 1350864 200 NISIKEAMKKLSDREKMILNMRff----dGRTQMEVADEIgiSQAQVSRLEKTALKHMK 254
gi 133469  196 QLMLQSVLHVLSDREKQIIDLTyi----qNKSQKETGDILgiSQMHVSRLQRKAVKKLR 250
gi 585925  226 RDLVRHLLVQLPEREQRILLLRyy----sNLTQSQISAELgvSQMHVSRLLARSFQRLR 280
gi 133474  193 KIALKEAISDLEEREKLIVYLRyy----kDQTQSEVAERLgiSQVQVSRLEKKILKQIK 247
gi 133475  201 ELALKEGMRRLNDREKMILRKRff----qGKTQMEVAEEIgiSQAQVSRLEKAAIKQMN 255

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