2NN6


Conserved Protein Domain Family
S1_Rrp40
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cd05790: S1_Rrp40 
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S1_Rrp40: Rrp40 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".
Links
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Statistics
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PSSM-Id: 240216
Aligned: 20 rows
Threshold Bit Score: 107.345
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_G       122 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLsfega-tkrnRPNVQVGDLIYGQFVVAnkd--mePEMVCIdsc 198 human
NP_565592     71 RYVPRPEDHVLGIVVDCKGENYWIDIKGPQLALLPVLafega-nrrnYPKFEVSTLLYTRVVKTntg--mnPELSCVdes 147 thale cress
NP_593242     71 RYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNALafenv-trksRPNLNVGSLVYARVSLAdrd--mePELECFdat 147 Schizosaccharom...
XP_366767     68 RYVPEPNDLVIGQVHHSSADFHFVTLAPHTTNALLPVlafegatrktRPVLPAGSLVYARVASAsrh--mdAELECFsqt 145 Magnaporthe gri...
BAD72364      70 RYIPSVEDTVLGVVVDTKPDNFLVDIKGPNLAFLPVLafegg-trrnIPKFEIGTLIYARVVKAnsi--mnPELSCMdat 146 Japanese rice
AAW27580     145 VGQFQPEDKVIGIVLKKAGELFVVDIGCASPATLNYLsfegs-skknRPDIHAGDVLYAMITRAdrd--leIELSCVdet 221 Schistosoma jap...
XP_570241     77 RYIPAQKDIVLGIIIARHADGYRVDLGSSQMAQLDALafega-tkrsKPNLKVGTLVFARVMSAsrd--mePELECFdpn 153 Cryptococcus ne...
XP_955675     50 RYQPCIDDIVIGKVVLTSQDMHKVDLGGTVGALPSLSftna--tkrnKPEVSKGDHLLCKIVRMgt----ePLLTCVg-- 121 Encephalitozoon...
XP_965833     67 RYIPSQGDLIIGQIARSATDFYYVSLSPYTPNATLPHlafesatkktRPQLASGELVYARVSLAnrh--mdPELECVnss 144 Neurospora cras...
XP_001611548  32 LYRPKIGDHVIGVVVAKNSDFYSLDIGGLTEAILPAVdgfrgatkrnRPNINEGDVIFCQITKQyprnelpVEVSCLdvd 111 Babesia bovis T2Bo

Feature 1                       
2NN6_G       199 g------ranGMGVI 207 human
NP_565592    148 g------kaaGFGPL 156 thale cress
NP_593242    148 t-----gkaaGYGEL 157 Schizosaccharomyces pombe 972h-
XP_366767    146 t-----gkadGLGPL 155 Magnaporthe grisea 70-15
BAD72364     147 g------kaaEFGQL 155 Japanese rice
AAW27580     222 g------kacGMGIL 230 Schistosoma japonicum
XP_570241    154 t-----gksdGFGEL 163 Cryptococcus neoformans var. neoformans JEC21
XP_955675    122 ---------eGFGKL 127 Encephalitozoon cuniculi GB-M1
XP_965833    145 t-----gkadGLGPL 154 Neurospora crassa OR74A
XP_001611548 112 dmkqwttketYFGSL 126 Babesia bovis T2Bo

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