2B63,1GO3,2CKZ


Conserved Protein Domain Family
RNAP_Rpb7_N_like
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cd00655: RNAP_Rpb7_N_like 
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RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Links
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Statistics
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PSSM-Id: 238354
Aligned: 4 rows
Threshold Bit Score: 111.792
Created: 24-Sep-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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protein
Conserved site includes 14 residues -Click on image for an interactive view with Cn3D
Feature 1:protein interaction surface [polypeptide binding site]
Evidence:
  • Comment:This is the surface by which Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP heterodimerize with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, and RpoE to RpoF).
  • Structure:1GO3_MN; Methanocaldococcus jannaschii RpoE N-terminal RNP domain binds RpoF; defined using 3.5A contacts.
    - View structure with Cn3D
  • Structure:2CKZ_AB; Saccharomyces cerevisiae Rpc25 N-terminal RNP domain (tip domain) binds the tip-associated domain of Rpc17; defined using 3.5A contacts.
    - View structure with Cn3D
  • Structure:2B63_DG; Saccharomyces cerevisiae Rpb7 binds Rpb4; defined using 3.5A contacts.
    - View structure with Cn3D
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1     ##### #                          #      #   ###                           #    #
2B63_G      2 FFIKDLSLNITLHPsfFGPRMKQYLKTKLLEEVEGSCtgKFGYiLCVLDydNIDI-QRGRIlpTDGSAEFNVKYRAVVFK 80  baker's yeast
1GO3_M      2 YKILEIADVVKVPPeeFGKDLKETVKKILMEKYEGRLdkDVGFvLSIVD--VKDI-GEGKVvhGDGSAYHPVVFETLVYI 78  Methanocaldococcus...
2CKZ_B      2 FILSKIADLVRIPPdqFHRDTISAITHQLNNKFANKIipNVGLcITIYD--LLTV-EEGQLkpGDGSSYINVTFRAVVFK 78  baker's yeast
EAT39485   28 VQKLEWTNLVSVLPkyLGDICEGVKACLTQKIGKYDRt-VDGIiLAFKN--TKILsPLSAIrpNSVRIHVKVSSNFYVFR 104 yellow fever mosquito

Feature 1      # 
2B63_G     81 PFK 83  baker's yeast
1GO3_M     79 PEM 81  Methanocaldococcus jannaschii
2CKZ_B     79 PFL 81  baker's yeast
EAT39485  105 PIS 107 yellow fever mosquito

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