2PMZ


Conserved Protein Domain Family
RNAP_D

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cd07030: RNAP_D 
Click on image for an interactive view with Cn3D
D subunit of Archaeal RNA polymerase
The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It 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 assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Statistics
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PSSM-Id: 132908
View PSSM: cd07030
Aligned: 23 rows
Threshold Bit Score: 301.109
Threshold Setting Gi: 15790216
Created: 19-Dec-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 23 residues -Click on image for an interactive view with Cn3D
Feature 1:D - L heterodimer interface [polypeptide binding site]
Evidence:
  • Structure:2PMZ_D; Interface between the Sulfolobus solfataricus RNAP subunit D and the L subunit (2PMZ_L); defined at 3.5A contacts.
    View structure with Cn3D
  • Comment:The assembly of the two largest RNAP subunits (A'/A" and B in archaea) depends on the presence of the D/L heterodimer.
  • Comment:The D subunit interfaces with the L subunit through its RPB11-like subdomain.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1         ####            #  ## ##  #  #    #                                            
2PMZ_D         1 MSINLLHKDd-TRIDLVFEGYPLEFVNAIRRASMLYvPIMAVDDVYFIENNs------------PLYDEILAHRLALIPF 67  Sulfolobus solf...
O59303         2 VKIKILKKTe-DSITFILEGVSVAFANALRRTILGEvPTFAVDEVEFYENDs------------ALFDEIIAHRLAMIPL 68  Pyrococcus hori...
YP_001738010   1 MKVRVIELSd-QRTLLVLEGVSPSFANSIRRAIIAEvPTFAIDEVIFFENTt------------PFFDEYIAHRLAMIPL 67  Candidatus Kora...
YP_001192208   1 MPIQVLKKEn-YFLSILTKDYPLEFVNSIRRASMLYvPVMAVDEVYVIENNs------------PLYDEMLAHRLGLIPF 67  Metallosphaera ...
NP_558758      1 MARATVVERgeYFLKAVVEGVPPSLVNSLRRVIISElPVMAIDNVVVVNNTs------------VMYDEMLAHRLGLIPL 68  Pyrobaculum aer...
YP_001040824   1 MEINVLEKTp-LRLRLYIKDIPLHVLNSIRRAIIAEvPTMAIDSVVFTMNSs------------VFYDEYIAHRLGLIPL 67  Staphylothermus...
YP_001012735   2 ARLCILDKDr-LTIRLYVEGFGLPLVNAIRRAAYSDvPVMAVDVVEVFENNt------------VLYDEIIAHRLGLIPL 68  Hyperthermus bu...
NP_394490      1 MDVKIFKLSd-KYIRFEIDGITPSQANALRRTLINDiPKLAIENVTFHHGEirdsegnvydsslPLFDEMVAHRLGLIPL 79  Thermoplasma ac...
NP_148137      7 RSVEVVELDs-LRVRLRIRGYPVVFVNAIRRTVLSDvPTMAVDYAYIFDNTt------------AVYDEMVAHRLGLVVL 73  Aeropyrum perni...
NP_280040      6 FDVEFVDRDd-REARFVVRNITPAFANGIRRAILVDvPTLSIDTVRFVENSs------------VMFDEQLGLRLGLVPL 72  Halobacterium s...
Feature 1                                                                                        
2PMZ_D        68 MSEealdtyrwp---eeciectenCEKCYTKIYIEAEAPne---pRMIYSKDIKSE-DPSVVPISGDIPIVLLGTNQKIS 140 Sulfolobus solf...
O59303        69 KTPtdrfe-----------ldaleLDDYTVTLSLEAEGP------GIVYSGDLKSD-DPDVKPVTPDIPIVKLAKGQRLV 130 Pyrococcus hori...
YP_001738010  68 RTSldv---------------lrvDPNRTVVLELSKKAKdp---iEVVYSGELKSS-DPLIYPANDKIPIIKMRKGQKLR 128 Candidatus Kora...
YP_001192208  68 DSKdaldyyrrp---eeciectenCDRCFTKAYIDVKAEds---qVMVYSRDIRTE-DPNVTPISKDIPIVLLGKNQKVT 140 Metallosphaera ...
NP_558758     69 TTPlqslppye-----dcvsgladPSECSTRLTLQVTAEg----dTTIYSGDLASD-RPDVVPVYKDIPIVKLVKGQSIV 138 Pyrobaculum aer...
YP_001040824  68 TSEaaldkykspeecreagdrglfTEDCFVKLDLEGKGEeg--klVTLHSGDLKTS-DPDVKPVYDNIPIIVLGKNQEIR 144 Staphylothermus...
YP_001012735  69 TSKealqkykrp---eecekaelgDPSCYVVLRLEVETGpr--eeRIVYSGDLETS-DPDVRPVYDNMPIVVMAPDQRLR 142 Hyperthermus bu...
NP_394490     80 KTDltmnfrdq------cscggkgCSLCTVTYSINKLGP------STVFSSDLQAVsHPDLIPVDGEIPIVKLGPKQAIL 147 Thermoplasma ac...
NP_148137     74 DSNeavekyrrp---eecagkepsEEDCFVEVSLEAEVDaegetgRYITAGDLSIS-DPQVKPVYPETPLIYVAPGQRIH 149 Aeropyrum perni...
NP_280040     73 TTPed------------------yAAGEAVTLALDVEGP------GTAYSGDLVSN-DPEVEAADENIPIIELKDDQRLE 127 Halobacterium s...
Feature 1                                                                                        
2PMZ_D       141 LEARLRLGYGKEHAKFIPVSLSVVRYYPk------VEILANC------EKAVNVCPegvfelkdg-----klsvknelsC 203 Sulfolobus solf...
O59303       131 FNAYAKLGRGKDHAKWQPGFTYYKYFTR-------VHISKKIng---wEKLAKLAKkrglptkene---eevivetikpF 197 Pyrococcus hori...
YP_001738010 129 FQAIARIGRGKDHSKWSPAAAVGYSYMPiyelkdpVECDLSQc-----SNCIESDGgisrv-------------dypvlC 190 Candidatus Kora...
YP_001192208 141 LEMKMRLGYGKEHAKFNPVSLAILRYKPk------VEVNKDC------EKAVEVCPervfsfeng-----klkvvnemaC 203 Metallosphaera ...
NP_558758    139 LEAYAKLGVAKDHAKWQAATASYYYYPKv------VVKSENCr-----EMCKEICRqlenp--------------iecsF 193 Pyrobaculum aer...
YP_001040824 145 LEAYARLGRGKEHAKWSPVSVAAHKYIAd------IYIDEKKclgencKKCIEVCPrnilsfengk---iivntnkifdC 215 Staphylothermus...
YP_001012735 143 LQAYARLGYGREHAKWMPVSVAAHRYLPile-fnlDEMSDEC------IRCIESGYpelaakiremrsgsiavvedvntS 215 Hyperthermus bu...
NP_394490    148 ITAEAILGTAKEHAKWQVTSGVSYKYHRe------FHVSKKDfe--dwQKLKGACPksvmsetd-------teivftddF 212 Thermoplasma ac...
NP_148137    150 VQAFARLGRGKEHTKWSPASLSVLRYTP-------ILIYDSSkagdecLECLSAYPqvvealksggk-gslvleglrrtS 221 Aeropyrum perni...
NP_280040    128 LEADAVMGHGRDHAKHQGGVAVGYRHLQr------VHVVGDS------PEYADDDPqmlrgviee------ddelvptdD 189 Halobacterium s...
Feature 1                                               #  #   #   # ###### # 
2PMZ_D       204 TLCEECLRYCn----gSIRISFVEDKYILEIESVGslKPERILLEAGKSIIRKIEELEKKL 260 Sulfolobus solfataricus
O59303       198 YIPKEFEEYEg----kEIWEEIVPDTYVFVVETNGelPVEEIVKIALRILMRKADRFINEL 254 Pyrococcus horikoshii
YP_001738010 191 EGCLEALERCrvrnpdKIIRRWDESRIIISYESTGslRPEEIFSEALNQVKGKLGELLNKI 251 Candidatus Korarchaeum cryptofilum...
YP_001192208 204 TLCEECVKACe-----GINVSPEPNQYILEIESVGslEPRRILIEATKSILSKIEELKKKV 259 Metallosphaera sedula DSM 5348
NP_558758    194 NKAWTCKDLCk----eGLEVTWDKNKYVFWVESFGnyDVNTALREAFRILKRKFAVFAEEL 250 Pyrobaculum aerophilum str. IM2
YP_001040824 216 SLCRICEEYCpt---dAIRVGWRENEYILTIESTGslPPKRILIEAVKILENKIDDFIENL 273 Staphylothermus marinus F1
YP_001012735 216 GLYWCVQRRCgg---kGVKLVYDDKRFILKIESTGalPPEDIVREAARAIVRKAENLLSQL 273 Hyperthermus butylicus DSM 5456
NP_394490    213 GCNDLNVLFEs----dGVNMIEDDSRFIFQFETDGslTAKETLLYALNRLKDRWDILVESL 269 Thermoplasma acidophilum DSM 1728
NP_148137    222 GLRYCAETACr----gAVEVRYDSSNLDLEVESTGalRPEKIVELAIRELEEKVKRFAEAV 278 Aeropyrum pernix K1
NP_280040    190 FDNDLTTRYPg----kEVEIEDVDGAFVFHVESDGsmPVEELVLRAVDTLVDRADELEQAV 246 Halobacterium sp. NRC-1

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