2NN6,2JEB,2BA0


Conserved Protein Domain Family
S1_Rrp4
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cd05789: S1_Rrp4 
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S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
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Statistics
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PSSM-Id: 240215
Aligned: 39 rows
Threshold Bit Score: 72.5822
Created: 17-Dec-2007
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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RNA bindingsubunit
Conserved site includes 4 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
Evidence:
  • Comment:RNA binding residues of the RNA PolymeraseII RPB7 subunit, confirmed by mutagenesis
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                   #       #         # #                                             
2NN6_H     90 RYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSsmnlpggelrrrsaedELAMRGFLQEGDLISAEVQAVfsd--g 167 human
2BA0_C     52 RYTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSenpe---------mkpNKKPNEVLDIGDAIIAKVLNIdpk--m 120 Archaeoglobus fulg...
AAB85189   57 KYIPKRGDVVIGEITDIRFSMWGLDINSPYTGLLPASevf----------gkdKRELESVFDIVDVLLLRVVDVdev--k 124 Methanothermobacte...
NP_394746  58 QYIPRKGDKVIGKVIEVGPSTWTVDINSPYFAMLHMNdtpw---------rmsSGDLKRYLNAGDYIYAKIMSVnei--k 126 Thermoplasma acido...
NP_559846  57 TYKPKKGDLVIGYVTDVLATGWEVDVRSFMPAYLPVGealhr------hvdleTTPLTTFLNIGDVVVAKVKDVdltdey 130 Pyrobaculum aeroph...
NP_616703  53 AYIPSANDVVIGIVIVVTPSNWIFDIAAPYDGLLHVSeypr---------rveSREMPEILNVGDSVILRVKDVdss--m 121 Methanosarcina ace...
NP_613667  61 PYRPSPGDFVVGIVEEVKFSSWLIDVRAPLPAILHVSnalee------evdliETDLSRYYRPGDVITAVVREVdpv--q 132 Methanopyrus kandl...
YP_448270  57 TYSPNYGDLVIGRVTGSSYSSWSIDINSTYHGFLPTTely----------dknEPNINNIINIKDMLLLRVANVdei--n 124 Methanosphaera sta...
YP_564958  52 KYIPSRKDFIIVNVIDVTPSNWIMETGSPYDGLLHVSefpk---------rvdSSEMRKFMDVGDCVIVRVKDVska--m 120 Methanococcoides b...
YP_843778  52 KYIPAVGDNVIGVVKDITFSNWILDINSPYDGLLHISefpk---------kidVEDMSKYLRIGSSVMARVKDVdpa--m 120 Methanosaeta therm...

Feature 1                        
2NN6_H    168 aVSLHTRs-----lKYGKL 181 human
2BA0_C    121 kVTLTMKd-----rICRPI 134 Archaeoglobus fulgidus
AAB85189  125 kVKLGLKg-----rGLGKF 138 Methanothermobacter thermautotrophicus str. Delta H
NP_394746 127 eSWLTLKe-----pGLKKL 140 Thermoplasma acidophilum DSM 1728
NP_559846 131 pIILTLKd-----eKVGKV 144 Pyrobaculum aerophilum str. IM2
NP_616703 122 kVELALRdpslhklKTGQI 140 Methanosarcina acetivorans str. C2A
NP_613667 133 rVELSLLedd-aptRLGRL 150 Methanopyrus kandleri AV19
YP_448270 125 rVKLTLRs-----rGLGKF 138 Methanosphaera stadtmanae DSM 3091
YP_564958 121 kVELSMReqgsralSKGRI 139 Methanococcoides burtonii DSM 6242
YP_843778 121 kVELTLNd-----rRLGVI 134 Methanosaeta thermophila PT

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