1XPP,1I50,2PMZ


Conserved Protein Domain Family
RNAP_RPB11_like

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cd07027: RNAP_RPB11_like 
Click on image for an interactive view with Cn3D
RPB11 subunit of RNA polymerase
The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L 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 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: 132905
View PSSM: cd07027
Aligned: 4 rows
Threshold Bit Score: 118.382
Threshold Setting Gi: 56967197
Created: 30-Dec-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 15 residues -Click on image for an interactive view with Cn3D
Feature 1:RPB11 - RPB3 heterodimer interface [polypeptide binding site]
Evidence:
  • Comment:The yeast RNAP II RPB11/RPB3 heterodimer (L/D heterodimer in archaea), together with RPB10 (N) and RPB12 (P), anchors the two largest subunits, RPB1 (A'/A") and RPB2 (B), stabilizing their association.
  • Structure:1I50_K; Saccharomyces cerevisiae RNAP II RPB11 subunit heterodimerizes with RPB3 subunit (1I50_C), defined using 3.5A contacts
    View structure with Cn3D
  • Comment:RPB11 (L) interfaces with the RPB11-like subdomain of RPB3 (D).
  • 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

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                        #    ### #    #             #                           ##    #
1XPP_A       13 LRViSKEk---NSITVEMINyDNTLLRTLVEEILKdDQVDEARYYIKHPviDNPQIYVRVKs-gKPQSAIKRAVRKLSKL 88
gi 82180681  14 VQA-QGNe--eSCVTFVLHEeDHTLGNSLRYMVMKnPEVEFCGYSITHPseTKINFRIQTRngiPAVEPFRRGLNELVDV 90
1I50_K       19 LKI-DPDtkapNAVVITFEKeDHTLGNLIRAELLNdRKVLFAAYKVEHPffARFKLRIQTTegyDPKDALKNACNSIINK 97
2PMZ_L        3 IRIlKSEs---NYLELEIEGeDHTLGNLIAGTLRRiSGVSFASYYQPHPlsDKIIVKILTDgsiTPKDALLKAIENIRGM 79

                ....*.
Feature 1       ## ###
1XPP_A       89 YEDLGT 94
gi 82180681  91 CQHVLN 96
1I50_K       98 LGALKT 103
2PMZ_L       80 TSHYID 85

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