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: 17-Jan-2013
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:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1       ###    ##       #   # ##  #  #                                                  
1I50_C        6 PQVKIREASkDNVDFILSNvDLAMANSLRRVMIAeiPTLAIDSVEVETNTtVLADEFIAHRLGLIPLQSMdieqleys-- 83
gi 18266895  49 FRVGVVQMDeDTLEFDMVGiDAAIANAFRRILLArvPTMAVEKVLVYNNTsIVQDEILAHRLGLIPILADprlfeyrnqg 128
2PMZ_D        1 MSINLLHKDdTRIDLVFEGyPLEFVNAIRRASMLyvPIMAVDDVYFIENNsPLYDEILAHRLALIPFMSEealdtyrwp- 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                       
1I50_C       84 --rdcfcedhCDKCSVVLTLQAFGese--------stTNVYSKDLVIvsnlm-----grniGHPIIqdkegnGVLICKLR 148
gi 18266895 129 eeegteidtlQFRLQVRCTRNPNAakdssdpnelyvnHKVYTRHMTWvplgnqadvfpegtIRPVHd-----DILIAQLR 203
2PMZ_D       80 -eeciectenCEKCYTKIYIEAEApn---------epRMIYSKDIKSed----------psVVPISg-----DIPIVLLG 134
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       ##                                                              
1I50_C      149 kgQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPwnklkhtdywyeqdsakewpq-----------------------sk 205
gi 18266895 204 pgQEIDLMMHCVKGIGKDHAKFSPVATASYRLLPaitllepvegeaaeelsqcfspgvieveevqgkkvarvanarldtf 283
2PMZ_D      135 tnQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPkveilancekavnvcpegvfelkdgkl-----------svknelsc 203
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*.
Feature 1                                          #   #  ##  #     ##  
1I50_C      206 nceyedppnegdpfdykaQADTFYMNVESVGsiPVDQVVVRGIDTLQKKVASILLA 261
gi 18266895 284 sreifrheklkkavrlarVRDHYIFSVESTGvlPPDVLVSEAIKILMGKCRRFLDE 339
2PMZ_D      204 tlceeclrycngsirisfVEDKYILEIESVGslKPERILLEAGKSIIRKIEELEKK 259

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