1IW7,1IW7,1I6V,1BDF,1BDF


Conserved Protein Domain Family
RNAP_alpha_NTD

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cd06928: RNAP_alpha_NTD 
Click on image for an interactive view with Cn3D
N-terminal domain of the Alpha subunit of Bacterial RNA polymerase
The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD.
Statistics
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PSSM-Id: 132904
View PSSM: cd06928
Aligned: 113 rows
Threshold Bit Score: 174.195
Threshold Setting Gi: 115531956
Created: 14-Nov-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 19 residues -Click on image for an interactive view with Cn3D
Feature 1:alphaNTD homodimer interface [polypeptide binding site]
Evidence:
  • Comment:Two alpha subunits of bacterial RNAP form a homodimer, which is equivalent to the RPB11/RPB3 and L/D heterodimer of yeast RNAP II and archaeal RNAP, respectively.
  • Comment:The bacterial RNAP alpha subunits homodimerize through their RPB11-like subdomains in the NTD.
  • Structure:1IW7_AB; Interface between two Thermus thermophilus RNAP alpha subunits, determined at 3.5A contacts.
    View structure with Cn3D
  • Structure:1BDF_AB; Interface between two Escherichia coli RNAP alpha subunits; defined at 3.5A contacts.
    View structure with Cn3D
  • Citation:PMID 9657722

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1       # #                #  # ###  #   #  ##   #                                      
1IW7_A       11 FTVRTQg-----rEYGEFVLEPLERGFGVTLGNPLRRILLSSipgTAVTSVYIEDvlHEFSTIPGVKEDVVEIILNLKEL 85
gi 11467399  11 SKVESSc-----nQYGRFIVEPLEPGQGITIGNSLRRVLLSDiegSAITAVRIAGvnHEFCSIPGVKEDVLELLLNLKNI 85
gi 41688691  17 STINHAr-----dIYAKFILQPLSYTQALTMGNSLRRVLLSElesISITAVRIAGasHELATLKGVREDVLQIMLNLKQI 91
gi 20139485  11 SNTEESr-----nHYSKFILEPLERGQGTTVGNALRRVLLSNlegTAVTAVRIAGvsHEFATVPGVREDVLEIIMRMKEV 85
gi 1710668   11 SRTDGAr-----gQYGSFVIEALNQGQGITLGNALRRSILSDlegTAIVAVRIAGvnHEFSTIPGVREDVLEILLNLKEV 85
gi 3914811   11 SKVYNAr-----dHWSRFVIDPLKPGQGTTLGNALRRTLLSElegLAITAVRIAGvsHEFSTINGIREDVLEILLNLKEI 85
gi 11465443  15 SMVINSr-----eIYGKFMIEPLSYGQAITVGNALRRVLLSDvpgVTIVSVRIAGinHEFSTVKGVKEDVLEILLNLKNI 89
gi 730608     6 IECIEStreglrdHYSKFCLEPLNQGQGTTLGNALRRTLLADlegTAIVAVRIAGvsHEFSTIPGIREDVLEILLNLKEV 85
gi 47679547  12 SERADSg-----eIYGQFQINDLNPGQGITIGTVLRRFLLSElnaTAITGVRIAGvnNEFSIIEGVREDVLELLLNLRPI 86
gi 13560647   7 CKCVDLdllntneFYGHFVFTALKKSQGNTIGNVLRRTLLSNlygFRIVGVRFAGinNEFALLEGVREDLFEIILNLKEI 86
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
1IW7_A       86 VVRFlnpslqTVTLLLKAEGpKEVKARDFLPva--dVEIMNPDLHIATLEeggrLNMEVRVDRGVGYVPAekh-gikDRI 162
gi 11467399  86 VLKSyt--nePQIGRLKIQGaCKVTTANFELps--eVEIIHGTQYVATVAenaiLEMEFKIEKGRGYKIIdkk-qteNSI 160
gi 41688691  92 VWRGqlk-kqPTITRLKVQGpAIVTAAAFQSeanssANIIDTCQYIATIDtqdiLEMECQLEQSSGYRLAkp----sEMI 166
gi 20139485  86 ILKSys--sqAQIGRLLVNGpTTITASHFDLps--eVEVIDPTQYVATIAeggkLEMEFRIERGKGYRTVergreeaTSL 161
gi 1710668   86 VFKSnn--qeSQIGRIKVQGpAIVTAGLFELss--dIEVVDPRQYIATICnntiFEMEFKIEKSCGYRLAeka-vdeLSL 160
gi 3914811   86 VFSGql--qeSTIGRLTVQGpAIVTARSFELpp--eIKLIDPEQYIATICgnntLEMEFKIEVGSGYKIVekd-nstEHF 160
gi 11465443  90 VLKGnv--lkNQIGRLKVQGpAIVTSGQIEFpl--dITVVDPCQYIATISgndyLEMELKVEKSSGYKLVetf-skkSPL 164
gi 730608    86 VLKSqi--gtSGVGRLRVQGpAIVTTNHLELps--eIELIDPNQYIATICgnniLEMEFRIETGKGYNLVerd-sdeSSI 160
gi 47679547  87 VIKNnsdnseMKFGRLKVQGpAVITANAIQLpt--eLEILNPNQYIATISrsmiLEMEFKFESGIGYRLVnqt-kmeSSS 163
gi 13560647  87 IILNsnridqTCYGRLKVYGpAVITAGSLELpn--nVKILNPNNHLLTISdeslIEIEVKIEAGKSYILAkdq-kleGAL 163
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|...
Feature 1                                                           #  ## ## ##
1IW7_A      163 NAIPVDAVfSPVRRVAFQVEDTRlgqrtDLDKLTLRIWTDGsVTPLEALNQAVEILREHLTYF 225
gi 11467399 161 DFLPIDAIfMPVRKVNYMVEEIFlrnseIKERLILEIWRNGsVTPQDSISQAAEVLLNLFNPF 223
gi 41688691 167 DWLPIDGVfMPVKRVNFWVDKALvdkvlVDKALHLEIWTNGsISPQEALHQAARILTHWFNPL 229
gi 20139485 162 DFLQIDSIfMPVRKVNYSVEEVRadgsiPKDRLLLEVWTNGsISPQEALSSAAGILVDLFNPL 224
gi 1710668  161 DFLQVDSVfMPVNKVNYKVEEVRvgtnsIKDRLILQIWTNGsISPQEAISQGATVLTNLFCSL 223
gi 3914811  161 EFLQVDSVfMPVKKVNFRIEETRgenniLNEQLILDIWTNGsISAKEAISNAADNLINLFSPL 223
gi 11465443 165 DFLPIDSIfMPVKKVNYYVEEILds-kvAYEKLILELWTNGsLSPQQSINYASDNLVKLFNPL 226
gi 730608   161 DFLQVDAIfMPVKKVNYLSKDIRsennlIQEQLTLEVWTNGsIDPQDAVSQAGKILTELLFPL 223
gi 47679547 164 DFLEIDAVfMPVQKVDFKVENIYdknkhISENLIIDIWTNGsISPETALYESSNNIIELFNSL 226
gi 13560647 164 DFIPIDSNfAPVLKVNWYIISLPqdgesINEELHLEIYTNGtLLPHQALLQARTMIGYMLSPI 226

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