1I50,1XPP,1IW7,1I50,2PMZ,1BDF,2PMZ,1IW7,1BDF


Conserved Protein Domain Family
RNAP_RPB11_RPB3

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cd00460: RNAP_RPB11_RPB3 
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RPB11 and RPB3 subunits of RNA polymerase
The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, 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. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts.
Statistics
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PSSM-Id: 132901
View PSSM: cd00460
Aligned: 10 rows
Threshold Bit Score: 56.6598
Threshold Setting Gi: 14278337
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
dimer interface
Conserved site includes 16 residues -Click on image for an interactive view with Cn3D
Feature 1:dimer interface [polypeptide binding site]
Evidence:
  • Comment:The eukaryotic RNAP II RPB11 and RPB3 subunits form a heterodimer, which is involved in RNAP assembly. The dimer stabilizes the association of the two largest RNAP subunits, RPB1 and RPB2. In archaea, the equivalent dimer is composed of subunits L and D. In bacteria, the equivalent dimer is a homodimer of alpha subunits.
  • Comment:RPB11 (subunit L in archaea) interfaces with the RPB11-like subdomain of RPB3 (subunit D in archaea). The bacterial alpha subunit homodimerizes through its RPB11-like subdomain.
  • Structure:1I50; Saccharomyces cerevisiae RNAP II RPB11 subunit (1I50_K) heterodimerizes with RPB3 subunit (1I50_C); defined using 3.5A contacts.
    View structure with Cn3D
  • Structure:1PMZ_L: Sulfolobus solfataricus RNAP L subunit heterodimerizes with the D subunit (1PMZ_D), determined at 3.5 A contacts.
    View structure with Cn3D
  • 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     # #              #       # ##  #  #                                             
1I50_K     19 LKI-DPDtkapNAVVITFEKe----DHTLGNLIRAELLNd---------------------------------------- 53  baker's yeast
1XPP_A     13 LRViSKEk---NSITVEMINy----DNTLLRTLVEEILKd---------------------------------------- 45  Thermoplasma acido...
1IW7_A     11 FTV-RTQg--rEYGEFVLEPlergfGVTLGNPLRRILLSsipgtavtsvyiedvlhefstipgvkedvveiilnlkelvv 87  Thermus thermophilus
Q5XK67     14 VQA-QGNe--eSCVTFVLHEe----DHTLGNSLRYMVMKn---------------------------------------- 46  African clawed frog
1I50_C      8 VKIrEASk---DNVDFILSNv----DLAMANSLRRVMIAeiptlaidsvevetnttvladefiahrlgliplqsmdieql 80  baker's yeast
2PMZ_L      3 IRIlKSEs---NYLELEIEGe----DHTLGNLIAGTLRRi---------------------------------------- 35  Sulfolobus solfata...
1BDF_A     14 VDI-EQVs--sTHAKVTLEPlergfGHTLGNALRAILLSsmpgcavteveidgvlheystkegvqedileillnlkglav 90  Escherichia coli
2PMZ_D      3 INLlHKDd---TRIDLVFEGy----PLEFVNAIRRASMLyvpimavddvyfiennsplydeilahrlalipfmseealdt 75  Sulfolobus solfata...
1IW7_B     11 FTV-RTQg--rEYGEFVLEPlergfGVTLGNPLRRILLSsipgtavtsvyiedvlhefstipgvkedvveiilnlkelvv 87  Thermus thermophilus
1BDF_B     14 VDI-EQVs--sTHAKVTLEPlergfGHTLGNALRAILLSsmpgcavteveidgvlheystkegvqedileillnlkglav 90  Escherichia coli
Feature 1                                                                                     
1I50_K        --------------------------------------------------------------------------------     baker's yeast
1XPP_A        --------------------------------------------------------------------------------     Thermoplasma acido...
1IW7_A     88 rflnpslqtvtlllkaegpkev------kardflpvadveimnpdlhiatleeggrlnmevrvdrgvgyvpaekhgikdr 161 Thermus thermophilus
Q5XK67        --------------------------------------------------------------------------------     African clawed frog
1I50_C     81 eysrdcfcedhcdkcsvvltlqafgesesttnvyskdlvivsnlmgrnighpiiqdkegngvlicklrkgqelkltcvak 160 baker's yeast
2PMZ_L        --------------------------------------------------------------------------------     Sulfolobus solfata...
1BDF_A     91 rvqgkdeviltlnksgigpvtaa---dithdgdveivkpqhvichltdenasismrikvqrgrgyvpastrihseederp 167 Escherichia coli
2PMZ_D     76 yrwpeeciectencekcytk---------iyieaeapneprmiyskdiksedpsvvpisgdipivllgtnqkislearlr 146 Sulfolobus solfata...
1IW7_B     88 rflnpslqtvtlllkaegpkev------kardflpvadveimnpdlhiatleeggrlnmevrvdrgvgyvpaekhgikdr 161 Thermus thermophilus
1BDF_B     91 rvqgkdeviltlnksgigpvtaa---dithdgdveivkpqhvichltdenasismrikvqrgrgyvpastrihseederp 167 Escherichia coli
Feature 1                                                                                     
1I50_K     54 ----------RKVLFAAYKVEHpf----------------------------------------------------fARF 71  baker's yeast
1XPP_A     46 ----------DQVDEARYYIKHpv----------------------------------------------------iDNP 63  Thermoplasma acido...
1IW7_A    162 inaipvdavfSPVRRVAFQVEDtrlgq----------------------------------------------rtdlDKL 195 Thermus thermophilus
Q5XK67     47 ----------PEVEFCGYSITHps----------------------------------------------------eTKI 64  African clawed frog
1I50_C    161 kgiakehakwGPAAAIEFEYDPwnklkhtdywyeqdsakewpqs------------knceyedppnegdpfdykaqaDTF 228 baker's yeast
2PMZ_L     36 ----------SGVSFASYYQPHpl----------------------------------------------------sDKI 53  Sulfolobus solfata...
1BDF_A    168 igrllvdacySPVERIAYNVEAarveq----------------------------------------------rtdlDKL 201 Escherichia coli
2PMZ_D    147 lgygkehakfIPVSLSVVRYYPkveilancekavnvcpegvfelkdgklsvknelsctlceeclrycngsirisfveDKY 226 Sulfolobus solfata...
1IW7_B    162 inaipvdavfSPVRRVAFQVEDtrlgq----------------------------------------------rtdlDKL 195 Thermus thermophilus
1BDF_B    168 igrllvdacySPVERIAYNVEAarveq----------------------------------------------rtdlDKL 201 Escherichia coli
Feature 1                     #  #   # #####
1I50_K     72 KLRIQTTegyDPKDALKNACNSIINKLGAL 101 baker's yeast
1XPP_A     64 QIYVRVKs-gKPQSAIKRAVRKLSKLYEDL 92  Thermoplasma acidophilum
1IW7_A    196 TLRIWTDgsvTPLEALNQAVEILREHLTYF 225 Thermus thermophilus
Q5XK67     65 NFRIQTRngiPAVEPFRRGLNELVDVCQHV 94  African clawed frog
1I50_C    229 YMNVESVgsiPVDQVVVRGIDTLQKKVASI 258 baker's yeast
2PMZ_L     54 IVKILTDgsiTPKDALLKAIENIRGMTSHY 83  Sulfolobus solfataricus
1BDF_A    202 VIEMETNgtiDPEEAIRRAATILAEQLEAF 231 Escherichia coli
2PMZ_D    227 ILEIESVgslKPERILLEAGKSIIRKIEEL 256 Sulfolobus solfataricus
1IW7_B    196 TLRIWTDgsvTPLEALNQAVEILREHLTYF 225 Thermus thermophilus
1BDF_B    202 VIEMETNgtiDPEEAIRRAATILAEQLEAF 231 Escherichia coli

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