2PMZ


Conserved Protein Domain Family
RNAP_A''

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cd06528: RNAP_A'' 
Click on image for an interactive view with Cn3D
A'' subunit of Archaeal RNA Polymerase (RNAP)
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Statistics
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PSSM-Id: 132725
View PSSM: cd06528
Aligned: 20 rows
Threshold Bit Score: 442.075
Threshold Setting Gi: 20094122
Created: 5-Oct-2007
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 69 residues -Click on image for an interactive view with Cn3D
Feature 1:Rpb1_C (A") - Rpb1_N (A') interaction site
Evidence:
  • Comment:The A' and A" complex of archaeal RNAP is equivalent to the largest subunit of eukaryotic and bacterial RNAPs. The A' and A" subunits correspond to the N-terminal two-thirds and the C-terminal one-third, respectively, of RNAPII Rpb1.
  • Structure:2PMZ; Interface between the A" (2PMZ_C) and A' (2PMZ_A) subunits of Sulfolobus solfataricus RNAP; defined at 3.5A contacts.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1             #  #   #    #                             #  #   ### ##     ### ###### ### #
2PMZ_C         25 IVDDLKNLILNKEIIVTrd------------------------eiDKIFDLAIKEYSEGL----IAPGEAIGIVAAQSVG 76   Sulfolobus so...
NP_613969       1 MNVEELLEEVCKEEDVElpdsvhreivek-----vsedeelkdadEETVRKVLRALVRNYkcrqIERGDAVGVLAAQSMC 75   Methanopyrus ...
AAR39272        6 EKILQEFEEMAKKYKIRgk------------------------kkEQLLKKLEEKYLNSL----IDPQEPIGIITAQSFG 57   Nanoarchaeum ...
Q8ZYQ7         18 PLYKEVEEAVRDLDDEKa---------------------------LRLVYRVLKLYVTSL----IDPGEAIGIVTAQSIG 66   Pyrobaculum a...
YP_001013741   35 DELVEKLKATTEKHGLTpe------------------------eaKKIIVNVLYEYEYSK----VEPGEPVGTVAAQSIG 86   Hyperthermus ...
ABK78186      896 PRMKEIVTGALAECGLSke------------------------gaEKVGKKGLDLYNKAK----VEPGQAVGIVTAQSIG 947  Cenarchaeum s...
Q9YAU2         21 SLYKELVETVEKEDGLSee------------------------dkISVVKETIRTYLRSL----AQPGEAVGTVAAQSIG 72   Aeropyrum pernix
YP_919697       5 ISEEELWNEIEKYHELLpaslrrelydk------ilkaglsrseaLSVINEALRRYLSSL----VSPGEAVGMVAAQSIG 74   Thermofilum p...
YP_001040813   29 EELREKLKEAYKEHGLYie------------------------evKAIIKETIDRYMRSQ----AEPGEPVGTVAAQSIG 80   Staphylotherm...
YP_001434835   13 KLIDEWERKLYEEYNIRskpkfieelrrnieklidvkpevseeelKKVVDLTFRYFLRAQ----VEPGEAVGTVAAQSIG 88   Ignicoccus ho...
Feature 1         ####  #                     #   #                                               
2PMZ_C         77 EPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKkvPSTPMMTIYLTDeyk--rdRDKALEVARKLEYTKIenvVSSTS 154  Sulfolobus so...
NP_613969      76 EPATQMTMRTFHLAGVAEIDITTGMPALERVLSLPy-HGPPTWVIELRLkepyrsdREKAEGVARKIEETRFeelTEYIE 154  Methanopyrus ...
AAR39272       58 EPATQMLLNAFHFAGVSELQLVTGLPRLIEILNAKkkPTIPSMTIYLEKn-----dEKLAEELVNKLIEVKLsdiAKSIS 132  Nanoarchaeum ...
Q8ZYQ7         67 EPGTQMILRSFHYAGLREFSMARGLPRLIEVVDARrtPSTPLMYVYLKPpyn--ksREAAESVAKKIQQVTLetlAKEVD 144  Pyrobaculum a...
YP_001013741   87 EPGTQMTLRTFHYAGIREFNVTLGLPRFIELVDARrePSTPIMHIYLDEehr--ydENKAKEVARRIEFTRVinvASEVD 164  Hyperthermus ...
ABK78186      948 EPGTQMTLRTFHFAGIKERNVTLGLPRLIELVDARkkPVTPTMDIHLDGesk--gsRDRAIEIAKNVLQTKIsalIADMD 1025 Cenarchaeum s...
Q9YAU2         73 EPGTQMTLRTFHYAGIMEFDVTLGLPRLIEIVDAKqtPSQPLMYIYLKDeya--kdLEKAKEAARKIEYTTLekiIDNIE 150  Aeropyrum pernix
YP_919697      75 EPATQMTLRTFHFAGVRELNVTLGLPRLIEIVDLRrePSTPIMEVYLEPeha--kdLDFALKIAREIELTTMenlCSSIT 152  Thermofilum p...
YP_001040813   81 EPSTQMTLRTFHYAGVREFNVTLGLPRLIEIVDARkkPGTPIMEIPLDEehk--ydEEKAKKVARMIESTTIeniSKEIN 158  Staphylotherm...
YP_001434835   89 EPSTQMTLRTFHYAGVKELNVTLGLPRLIEIVDARrtPSTPTMTVYLDEehr--hdKEKALEVARKIEMTKVenvASSVE 166  Ignicoccus ho...
Feature 1                                                                                         
2PMZ_C        155 IDIASmsIILQLDNEMLKDKGVTVDDVKKAIGRlklgdfmieese---------------dstlninfanidSIAALFKL 219  Sulfolobus so...
NP_613969     155 VNPDEcaIEIGLDEERIEEHGIDEDQLVAFVREhtggachlegd------------------vlkvtladveSASELAEI 216  Methanopyrus ...
AAR39272      133 IDVINkrIIIELDQQLVKEKDITKKDLEKAFKSaklkakienn--------------------titieagnkRPKELYLL 192  Nanoarchaeum ...
Q8ZYQ7        145 VDYVAgtVTITLDQEQLKYRGLTLKDVEKIVAKakgkdvaismr-----------------gytitaslttpDILKIRKI 207  Pyrobaculum a...
YP_001013741  165 IDLVNmrMVIKLDPVMLEDKGVTVEQVKKALERlklgkveqdpsnp-------------lvlyipieisegfSIIDLQKK 231  Hyperthermus ...
ABK78186     1026 TDYSTq-IRLGLDEGKMDDRGCTPDDVAAALASnkkfkvsvegr------------------rltldmaeeyDAPAVIAV 1086 Cenarchaeum s...
Q9YAU2        151 WDLGDrvVAIVINAEYMEDKGVTVDMVLEALDKsklgkvvedgvrevseggvkkvivyfeisdkqlpdeelfNSNAYHKV 230  Aeropyrum pernix
YP_919697     153 IDYFEfaIVMELDPDMMENRGVTMDDVINALEKlkgkkgkievn-----------------gntvvlytgleDVTKLRRM 215  Thermofilum p...
YP_001040813  159 VDPYEg-ATIVLDSEMLSDKGISVDEVVKVLEKlklgkvyvdpedp--------------yvihialrsekiDYTKVEKI 223  Staphylotherm...
YP_001434835  167 IDWFEttIIVRLDPEMMEDKGITRDDVIKAINRlrikgraepdpdde------------yavlvrldpeaytSIGELQKV 234  Ignicoccus ho...
Feature 1                                                                                         
2PMZ_C        220 RDKILNTKIKGIKGIKRAIVQKKgd------eYIILTDGSNLSGVLSVK--------------------------GVDVA 267  Sulfolobus so...
NP_613969     217 ANDLREAVVKGIEGVLHASVQYDede----eeYYILVRGSPEGAPGRPPrwisqrarnskvakraylmlqlmqldEVDAT 292  Methanopyrus ...
AAR39272      193 KNKIKDLHIKGVKGIKYAMITREnd------eLVIKTFGSNLKEVLKMK--------------------------GIDKT 240  Nanoarchaeum ...
Q8ZYQ7        208 KDKILQIKISGIKGVRKVVLQYDskn----deWYIVTEGTNLEAVLQLE--------------------------EVDPT 257  Pyrobaculum a...
YP_001013741  232 REKILNAKIKGIRKIRRVIIQSItgpd-grteYFLVTEGSNLKEVLEVP--------------------------GVDPR 284  Hyperthermus ...
ABK78186     1087 RNKVLNTTVKGVPDVERLTLVQKdd------eWVIQTTGSNLPKVLAVE--------------------------GIDKR 1134 Cenarchaeum s...
Q9YAU2        231 LEKLKNTYIKGIKGIRKVTVRREeged--syeYMLIVEGSNLREVLMLP--------------------------EVDHR 282  Aeropyrum pernix
YP_919697     216 YDRVLNLRIKGLKGIRHAIVKPVrdekgelveYVILTEGSNLKAVLGIE--------------------------GVDPR 269  Thermofilum p...
YP_001040813  224 RTKIANTKIKGIKGITKVIIQKRgd------eYILVAEGSNLAEVMKVP--------------------------GVDYR 271  Staphylotherm...
YP_001434835  235 RDKVLSAKIKGIKGINRVIVQQRed------eYVLVTDGSNLAQVLEVE--------------------------GVDPT 282  Ignicoccus ho...
Feature 1                                             ### ## ### ##  #      #    ##      # #    # 
2PMZ_C        268 KVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTg---eKNSVLARAAF 344  Sulfolobus so...
NP_613969     293 RVNTNDPKIVDVLLGVEAGRNAIIEQLEEVYESQGISVDPRHFMLISDMMSFWGELRSVRSVGGYsvmelKGSPLTKAAF 372  Methanopyrus ...
AAR39272      241 RTTTNDIHEIAKVLGIDAAREAIIEEIQKVLEEQGLEIDVRYLLLIADVMTYYGEVLGFTRHGLMe---rKPSPLERATF 317  Nanoarchaeum ...
Q8ZYQ7        258 RTYSNDLHEVEEVLGIEATRALVAQEIKRVLEEQGLDVDIRHMYLVADAMTWSGRLRPIGRHGVVg---sKESPLARAAF 334  Pyrobaculum a...
YP_001013741  285 RIYTNSIHEIEEVLGIEAARTMLIREMKDVLDEQGLDVDIRHLMLVADIMTMTGRVRQIGRHGVSg---eKPSPFARAAF 361  Hyperthermus ...
ABK78186     1135 QVRTNNVFEIAGTLGIEAARNALINELRSTLEDQGLEVDIRYIMLVSDLMCSRGYMQQIGRHGIAg---tKDSVLARAAF 1211 Cenarchaeum s...
Q9YAU2        283 RSISNDIQEIAQVLGIEAARTAIIEEIKRVLEDSGLDVDIRHLMLIADLMTWPGYVRQIGRLGVVg---eKPSPLARAAF 359  Aeropyrum pernix
YP_919697     270 RTTTNNILEIYEVLGIEAARAAIIKEIKKVLDEHGLDVDWRHIMMVADAMTYSGKVRQVGRHGVAg---eKGSVLARASF 346  Thermofilum p...
YP_001040813  272 KVYTNNIAEIEEILGIEAARAAIIRETKNVLEDQGLDVDIRHLILLADMMTWTGKIRQVGRMGIAg---eKPSVLARATF 348  Staphylotherm...
YP_001434835  283 RTVSDSIKEIEEVLGIEAARQAIINEILDVLENQGLDVDRRHIMLLADAMTWSGEVRQVGRHGIAg---tKPSVLARAAF 359  Ignicoccus ho...
Feature 1         # ##   ## ###### #######     #     # #       
2PMZ_C        345 EVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTMRP 389  Sulfolobus solfataricus
NP_613969     373 EYVSRVLTETATSGDVEELRGVLENIIVGKPVPVGTGTVELTVDY 417  Methanopyrus kandleri AV19
AAR39272      318 EVPFKNLADAALLGEKDDLRAVIVNVLINQPAPMGTGRIKLVFDE 362  Nanoarchaeum equitans Kin4-M
Q8ZYQ7        335 EVTVKTLIEASVRGEDELFKGVVESIIAGKYVPIGTGIVRLLMQF 379  Pyrobaculum aerophilum
YP_001013741  362 EMTTQNLYAAAVEGEVDRLLGVAETVIVGGVIRVGTGMVEVRMSP 406  Hyperthermus butylicus DSM 5456
ABK78186     1212 EITVPTIAHAALSGEVEHLRGVTENVIVGSNIPIGSGTVDLYMQV 1256 Cenarchaeum symbiosum A
Q9YAU2        360 EVTVKQLYEAAVWGEEEEFAGVTENIIAGLPPRVGTGSVLLRMGA 404  Aeropyrum pernix
YP_919697     347 EVTVKNLVEAALRGELDELRGVIENVIIGSKPIPLGTGSVKLKMR 391  Thermofilum pendens Hrk 5
YP_001040813  349 EMTVQKLVEAAVEGEVDMLKGVPENVIIGQPVPVGTGIVEIFMMP 393  Staphylothermus marinus F1
YP_001434835  360 EVTVKQLVDAAVEGEVDELKGVTENIIIGQPIPLGTGMVLLAMNP 404  Ignicoccus hospitalis KIN4/I

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