2B8K,3H0G


Conserved Protein Domain Family
Zn-ribbon_RPB9
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cd10508: Zn-ribbon_RPB9 
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C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II
The C-terminal zinc ribbon domain (C-ribbon) of subunit B9 (Zn-ribbon_RPB9) in RNA polymerase (Pol) II is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPB9 have strong homology to RPA12 of Pol I and RPC11 of Pol III subunits but its intrinsic cleavage activity is weaker for Pol II. Zn-ribbon_RPB9 is homologous to Pol II elongation factor TFIIS domain III. The very weak cleavage activity of Pol II is stimulated by TFIIS. RPB9 has two zinc-binding domains separated by a flexible linker.
Links
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Statistics
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PSSM-Id: 259793
Aligned: 60 rows
Threshold Bit Score: 61.8854
Created: 25-Sep-2006
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
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Zn binding sitetrimer
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 cysteines contact to one zinc ion at 4.0 A
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                    #  #                         #    #     
2B8K_I        64 SDPTLPRSD-RECPKCHSRENVFFQSQQrr-kDTSMVLFFVCLs--CSHIFT 111 baker's yeast
EEE22327      57 KDPTLGRVFdWRCPRCRGVGGVFYQLPErv-aEDAMTLVYVCTqpgCGAWEI 107 Toxoplasma gondii GT1
CBK21251     128 EDPTLSRDEnKECEECHEKGCVFFQAHGd--gDEAMALIFMCIh--CKHKWI 175 Blastocystis hominis
XP_002767499  77 HDPTLSRTTeYTCNNCPNHEAVFWQLPEsq-qTNAMALIFVCT---ACTAWR 124 Perkinsus marinus ATCC 50983
EGB02800      70 QDPTLQRSDhVSCDACGHHTAVLFQAESgv-tAVSLSLIFVCCa--CGNKWV 118 Aureococcus anophagefferens
XP_626758     70 QDPTLGRTLeWNCRGCGHNVAVFFQLPErv-cSEAMTLVFVCVs--CGEWVK 118 Cryptosporidium parvum Iowa II
XP_828806     76 NDPTAQRDTtKQCPRCAMNEVTCFVNPLgq-pHEDMTLYFACAnqgCRHVWK 126 Trypanosoma brucei brucei strain 927/4 GUTa...
CAD49061      67 NDPALGRVRdWVCKQCGNNEAVFLQLAEki-sYNPMALIYVCTnkhCHYWEK 117 Plasmodium falciparum 3D7
CAD36017      68 KDPCLARRIgKPCQKCGNTLAVTFTNPS----KERMNLISVCTq--CTHYWR 113 Sterkiella histriomuscorum
EED94762      62 DDPTLPRSQnAHCDKCGHNEAVFFQSDTsdvrNDTLALIFVCCn--CDHKWV 111 Thalassiosira pseudonana CCMP1335

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