1Y1V,2B8K,1QYP,1TFI


Conserved Protein Domain Family
Zn-ribbon
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cd00656: Zn-ribbon 
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C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit
The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.
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Statistics
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PSSM-Id: 259791
Aligned: 28 rows
Threshold Bit Score: 56.9372
Created: 24-Sep-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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Zn binding site
Conserved site includes 4 residues -Click on image for an interactive view with Cn3D
Feature 1:Zn binding site [ion binding site]
Evidence:
  • Comment:The zinc ribbon is the most conserved part of RPB9, RPC11, RPA12 subunits of RNA polymerases and it is homologous to TFIIS domain III and the C-terminal zinc ribbon domain of archaeal Transcription Factor S. Three antiparallel b-sheets are stabilized by a tetrad of cysteines that chelate zinc
  • Structure:2BBK_I: Saccharomyces cerevisiae C_ribbon domain of RPB9 , four cysteins contact to one zinc ion at 4.0 A
    - View structure with Cn3D
  • Structure:1QYP_A, Archaeal TFIIS (TFS) domain III contacts Zn ion at 4.0 A
    - View structure with Cn3D
  • Citation:PMID 9634694
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                 #  #                        #    #     
1Y1V_S       132 ERSVTDrfTCGkCKEKKVSYYQLQTrsaDEPLTTFCTCEa--CGNRWK 177 baker's yeast
2B8K_I        67 TLPRSDr-ECPkCHSRENVFFQSQQrrkDTSMVLFFVCLs--CSHIFT 111 baker's yeast
1TFI_A         3 GGTQTDlfTCGkCKKKNCTYTQVQTrsaDEPMTTFVVCNe--CGNRWK 48  human
NP_057394     61 NVDSTAe-SCPkCEHPRAYFMQLQTrsaDEPMTTFYKCCnaqCGHRWR 107 human
NP_055411     79 QGPVVDr-RCPrCGHEGMAYHTRQMrsaDEGQTVFYTCTn--CKFQEK 123 human
NP_394466     53 AEPLDSdaVCPrCHHKGARYVLKQTrsaDEPETKFYTCEe--CGYRWR 98  Thermoplasma acidophilum DSM 1728
NP_280494    172 GKPTAEe-TCPeCGHGEAWYTIKQTgsaDEPPTRFFKCQd--CGNRWR 216 Halobacterium sp. NRC-1
YP_003422915  84 MRSTVRe-ICPkCGHDRASYELLQTrsaDEAPTRFFTCEk--CHHKWR 128 Methanobrevibacter ruminantium M1
EHR77105      71 VLTTGTy-MCPkCDKMEVFSYLEQTrssDEPETRMLTCKn--CGHGWR 115 uncultured marine group II euryarchaeote
ELZ71823      48 IGPTTKt-ICPkCGHDVARYEMKQIrsaDESETRFFTCVe--CDHKWR 92  Haloferax gibbonsii ATCC 33959

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