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: 2-Oct-2020
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:
Feature 1     # #                #  # ###  #   #  ##   #                                      
1IW7_A     11 FTVRTQg-----rEYGEFVLEPLERGFGVTLGNPLRRILLSSipgTAVTSVYIEDvlHEFSTIPGVKEDVVEIILNLKEL 85  Thermus thermophilus
NP_043256  11 SKVESSc-----nQYGRFIVEPLEPGQGITIGNSLRRVLLSDiegSAITAVRIAGvnHEFCSIPGVKEDVLELLLNLKNI 85  Cyanophora paradoxa
Q85FU3     17 STINHAr-----dIYAKFILQPLSYTQALTMGNSLRRVLLSElesISITAVRIAGasHELATLKGVREDVLQIMLNLKQI 91  Cyanidioschyzon me...
Q8YPK3     11 SNTEESr-----nHYSKFILEPLERGQGTTVGNALRRVLLSNlegTAVTAVRIAGvsHEFATVPGVREDVLEIIMRMKEV 85  Nostoc sp. PCC 7120
P51293     11 SRTDGAr-----gQYGSFVIEALNQGQGITLGNALRRSILSDlegTAIVAVRIAGvnHEFSTIPGVREDVLEILLNLKEV 85  Porphyra purpurea
O46914     11 SKVYNAr-----dHWSRFVIDPLKPGQGTTLGNALRRTLLSElegLAITAVRIAGvsHEFSTINGIREDVLEILLNLKEI 85  Guillardia theta
NP_045166  15 SMVINSr-----eIYGKFMIEPLSYGQAITVGNALRRVLLSDvpgVTIVSVRIAGinHEFSTVKGVKEDVLEILLNLKNI 89  Cyanidium caldarium
Q01569      6 IECIEStreglrdHYSKFCLEPLNQGQGTTLGNALRRTLLADlegTAIVAVRIAGvsHEFSTIPGIREDVLEILLNLKEV 85  Pyrenomonas salina
AAT36717   12 SERADSg-----eIYGQFQINDLNPGQGITIGTVLRRFLLSElnaTAITGVRIAGvnNEFSIIEGVREDVLELLLNLRPI 86  Corethron hystrix
AAK30140    7 CKCVDLdllntneFYGHFVFTALKKSQGNTIGNVLRRTLLSNlygFRIVGVRFAGinNEFALLEGVREDLFEIILNLKEI 86  Fucus vesiculosus
Feature 1                                                                                     
1IW7_A     86 VVRFlnpslqTVTLLLKAEGpKEVKARDFLPva--dVEIMNPDLHIATLEeggrLNMEVRVDRGVGYVPAekh-gikDRI 162 Thermus thermophilus
NP_043256  86 VLKSyt--nePQIGRLKIQGaCKVTTANFELps--eVEIIHGTQYVATVAenaiLEMEFKIEKGRGYKIIdkk-qteNSI 160 Cyanophora paradoxa
Q85FU3     92 VWRGqlk-kqPTITRLKVQGpAIVTAAAFQSeanssANIIDTCQYIATIDtqdiLEMECQLEQSSGYRLAkp----sEMI 166 Cyanidioschyzon me...
Q8YPK3     86 ILKSys--sqAQIGRLLVNGpTTITASHFDLps--eVEVIDPTQYVATIAeggkLEMEFRIERGKGYRTVergreeaTSL 161 Nostoc sp. PCC 7120
P51293     86 VFKSnn--qeSQIGRIKVQGpAIVTAGLFELss--dIEVVDPRQYIATICnntiFEMEFKIEKSCGYRLAeka-vdeLSL 160 Porphyra purpurea
O46914     86 VFSGql--qeSTIGRLTVQGpAIVTARSFELpp--eIKLIDPEQYIATICgnntLEMEFKIEVGSGYKIVekd-nstEHF 160 Guillardia theta
NP_045166  90 VLKGnv--lkNQIGRLKVQGpAIVTSGQIEFpl--dITVVDPCQYIATISgndyLEMELKVEKSSGYKLVetf-skkSPL 164 Cyanidium caldarium
Q01569     86 VLKSqi--gtSGVGRLRVQGpAIVTTNHLELps--eIELIDPNQYIATICgnniLEMEFRIETGKGYNLVerd-sdeSSI 160 Pyrenomonas salina
AAT36717   87 VIKNnsdnseMKFGRLKVQGpAVITANAIQLpt--eLEILNPNQYIATISrsmiLEMEFKFESGIGYRLVnqt-kmeSSS 163 Corethron hystrix
AAK30140   87 IILNsnridqTCYGRLKVYGpAVITAGSLELpn--nVKILNPNNHLLTISdeslIEIEVKIEAGKSYILAkdq-kleGAL 163 Fucus vesiculosus
Feature 1                                                         #  ## ## ##
1IW7_A    163 NAIPVDAVfSPVRRVAFQVEDTRlgqrtDLDKLTLRIWTDGsVTPLEALNQAVEILREHLTYF 225 Thermus thermophilus
NP_043256 161 DFLPIDAIfMPVRKVNYMVEEIFlrnseIKERLILEIWRNGsVTPQDSISQAAEVLLNLFNPF 223 Cyanophora paradoxa
Q85FU3    167 DWLPIDGVfMPVKRVNFWVDKALvdkvlVDKALHLEIWTNGsISPQEALHQAARILTHWFNPL 229 Cyanidioschyzon merolae
Q8YPK3    162 DFLQIDSIfMPVRKVNYSVEEVRadgsiPKDRLLLEVWTNGsISPQEALSSAAGILVDLFNPL 224 Nostoc sp. PCC 7120
P51293    161 DFLQVDSVfMPVNKVNYKVEEVRvgtnsIKDRLILQIWTNGsISPQEAISQGATVLTNLFCSL 223 Porphyra purpurea
O46914    161 EFLQVDSVfMPVKKVNFRIEETRgenniLNEQLILDIWTNGsISAKEAISNAADNLINLFSPL 223 Guillardia theta
NP_045166 165 DFLPIDSIfMPVKKVNYYVEEILds-kvAYEKLILELWTNGsLSPQQSINYASDNLVKLFNPL 226 Cyanidium caldarium
Q01569    161 DFLQVDAIfMPVKKVNYLSKDIRsennlIQEQLTLEVWTNGsIDPQDAVSQAGKILTELLFPL 223 Pyrenomonas salina
AAT36717  164 DFLEIDAVfMPVQKVDFKVENIYdknkhISENLIIDIWTNGsISPETALYESSNNIIELFNSL 226 Corethron hystrix
AAK30140  164 DFIPIDSNfAPVLKVNWYIISLPqdgesINEELHLEIYTNGtLLPHQALLQARTMIGYMLSPI 226 Fucus vesiculosus

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