1I50,2PMZ


Conserved Protein Domain Family
RNAP_RPB3_like

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cd07028: RNAP_RPB3_like 
Click on image for an interactive view with Cn3D
RPB3 subunit of RNA polymerase
The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, 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. 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 RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to 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 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: 132906
View PSSM: cd07028
Aligned: 3 rows
Threshold Bit Score: 295.631
Threshold Setting Gi: 167744884
Created: 18-Dec-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 20 residues -Click on image for an interactive view with Cn3D
Feature 1:RPB3 - RPB11 heterodimer interface [polypeptide binding site]
Evidence:
  • Comment:The yeast RNAP II RPB11/RPB3 heterodimer, together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, stabilizing their association.
  • Comment:RPB3 (subunit D in archaea) associates with RPB11 (subunit L in archaea) through its RPB11-like subdomain.
  • Structure:1I50_C; Interface between the Saccharomyces cerevisiae RNAP II RPB3 and RPB11 (1I50_K) subunits; defined at 3.5A contacts.
    View structure with Cn3D
  • 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

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1     ###    ##       #   # ##  #  #                                                  
1I50_C      6 PQVKIREASkDNVDFILSNvDLAMANSLRRVMIAeiPTLAIDSVEVETNTtVLADEFIAHRLGLIPLQSMdieqleys-- 83  baker's yeast
P52432     49 FRVGVVQMDeDTLEFDMVGiDAAIANAFRRILLArvPTMAVEKVLVYNNTsIVQDEILAHRLGLIPILADprlfeyrnqg 128 house mouse
2PMZ_D      1 MSINLLHKDdTRIDLVFEGyPLEFVNAIRRASMLyvPIMAVDDVYFIENNsPLYDEILAHRLALIPFMSEealdtyrwp- 79  Sulfolobus solfata...
Feature 1                                                                                     
1I50_C     84 --rdcfcedhCDKCSVVLTLQAFGese--------stTNVYSKDLVIvsnlm-----grniGHPIIqdkegnGVLICKLR 148 baker's yeast
P52432    129 eeegteidtlQFRLQVRCTRNPNAakdssdpnelyvnHKVYTRHMTWvplgnqadvfpegtIRPVHd-----DILIAQLR 203 house mouse
2PMZ_D     80 -eeciectenCEKCYTKIYIEAEApn---------epRMIYSKDIKSed----------psVVPISg-----DIPIVLLG 134 Sulfolobus solfata...
Feature 1                     ##                                                              
1I50_C    149 kgQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPwnklkhtdywyeqdsakewpq-----------------------sk 205 baker's yeast
P52432    204 pgQEIDLMMHCVKGIGKDHAKFSPVATASYRLLPaitllepvegeaaeelsqcfspgvieveevqgkkvarvanarldtf 283 house mouse
2PMZ_D    135 tnQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPkveilancekavnvcpegvfelkdgkl-----------svknelsc 203 Sulfolobus solfata...
Feature 1                                        #   #  ##  #     ##  
1I50_C    206 nceyedppnegdpfdykaQADTFYMNVESVGsiPVDQVVVRGIDTLQKKVASILLA 261 baker's yeast
P52432    284 sreifrheklkkavrlarVRDHYIFSVESTGvlPPDVLVSEAIKILMGKCRRFLDE 339 house mouse
2PMZ_D    204 tlceeclrycngsirisfVEDKYILEIESVGslKPERILLEAGKSIIRKIEELEKK 259 Sulfolobus solfataricus

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