1YT3,2HBL,3CYM


Conserved Protein Domain Family
RNaseD_exo

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cd06142: RNaseD_exo 
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DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins
Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Statistics
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PSSM-Id: 176654
View PSSM: cd06142
Aligned: 104 rows
Threshold Bit Score: 129.19
Threshold Setting Gi: 45551159
Created: 26-Mar-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1:catalytic site [active site]
Evidence:
  • Comment:The catalytic site is characterized by the presence of four negatively charged residues (DEDD) that serve as ligands for the two metal ions required for activity.
  • Comment:DEDDy exonucleases contain a conserved tyrosine at the ExoIII motif which is important in catalysis.
  • Structure:1YT3_A; Escherichia coli RNase D binds two Zn ions.
    View structure with Cn3D
  • Structure:2HBL_A; Saccharomyces cerevisiae Rrp6p binds Mn and Zn in its catalytic site.
    View structure with Cn3D
  • Structure:3CYM_A; Bifidobacterium adolescentis Bad_0989 protein exonuclease domain binds two Na ions in its catalytic site.
    View structure with Cn3D
  • Citation:PMID 9396823

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                          # #                                                          
1YT3_A       11 ALASLCEAVr--aFPAIALDTEFVRtrtyyPQLGLIQLFdg------eHLALIDPLGit--dWSPLKAILRDps-----i 75  Escherichia coli
NP_104433     7 HKHDLPDLShy-nVGAVAIDTETLGlnphrDRLCLVQISpg-----dgSADVIQIAPgq-kkAPNLVSLLRNrs-----v 74  Mesorhizobium lo...
YP_758935     7 HKGDLPEGLs--lGPVIAVDTEAMGlnamrDNLTLVQVSsg-----dgTAHLVQLTRdy--dCPNLKALLTDpk-----v 72  Hyphomonas neptu...
NP_966626     6 YKDDLPASSipddIRSIAVDTEAMGllhsrDRLCLVQLSfn-----dgNAHLVQLKNdy--tAPNLRKILEDkn-----i 73  Wolbachia endosy...
NP_348532    10 DLDNNDKRYilnnCKYIAIDTETTGldplkDKLCLIQICak------eKIFLIKYNNs---nQKNLIGILQCsk-----i 75  Clostridium acet...
YP_872922   363 VTPDFLRYIy--sTGKAGWDIETTGlnwyaDRICTVQLAcg------nRVAVVQLPEgh--tPQRLSQILGDqn-----i 427 Acidothermus cel...
YP_265923     8 HKNDLPEDLd--lGNIIAVDGEFMGlnvkrDPLCLIQIStg-----nsDAHIIQLDRek-ydAPNLNKVLSDas-----i 74  Candidatus Pelag...
YP_425107    10 HRGDLPSGLt--fPQGIAVDTETMGlnphrDRLCVVQLSgg-----dnIAHVVHLNRdl--qAPVLASLLGDps-----v 75  Rhodospirillum r...
ZP_01631084   9 EIRGFISTLt--sHKTLWLDTEIADftthyPRLSLIQVLadptdstgvSAYLLDVLD-----KPDLAEYFINqiminpni 81  Nodularia spumig...
NP_485737     9 EIRAIVAGYt--qATTLWIDTEVADyksrnPRLSLIQVLddpndmsgdRVYLLDVLDqpdlvADFVDKIMVNtn-----i 81  Nostoc sp. PCC 7120
Feature 1                #                                                                      
1YT3_A       76 TKFLHAGSEDLEVFLNVFGel-pqPLIDT-QILAAFCGRp---mSWGFASMVEEYSg-VTLDKSESRTDWLARPLTeRQC 149 Escherichia coli
NP_104433    75 TKLFHFGRFDLAVLYNAFGvm-pePVFCT-KIASRLTRTyt--dRHGLKDICFELLg-VGLSKAQQSSDWAAETLSpEQL 149 Mesorhizobium lo...
YP_758935    73 LKIFHFARFDVVMMKRWMGit-caPIWCT-KIASRLARTyt--dRHGLKDVAREVAg-VDMSKAQQSSDWGQDKLTdAQI 147 Hyphomonas neptu...
NP_966626    74 TKIFHFARFDVSIIRYYLEtw-alPCYCT-KIASRLVRTyt--dNHSLKELCLELLd-TKLNKQQQSSDWGNENLTdKQK 148 Wolbachia endosy...
NP_348532    76 IKIFHHANFDLRFLMKNLKiyninNVVCT-KIAAKLLNGie--iENSLKKLLRKYLn-INIDKKLQKSNWSAENLTkEQI 151 Clostridium acet...
YP_872922   428 LKIFHNARFDLRFMVYHWSvi-pqNVACT-LELVRLLNPre-raGHTLREVLERYLa-VQIIKDQTCSDWTTAQLTqEQI 503 Acidothermus cel...
YP_265923    75 IKIFHYGRADMAHIKHYLKte-tnNILDT-KIASKLARSys--dSHSLKTLIKEFMn-VDVSKQFQSSDFGGELSP-AQL 148 Candidatus Pelag...
YP_425107    76 LKIMHFGRFDIASIHHGLGvl-cePVYCT-KIASKLCRTnt--dSHGLKALCKDLLg-VDLSKHQQTSDWGAESLSpEQL 150 Rhodospirillum r...
ZP_01631084  82 EKVFHNAGFDLKYLGKKLAq----NITCTyQIARKITRDrlkvsNLKLKTLAAELChfVNVDADEGSSDWGKRPLSdKQV 157 Nodularia spumig...
NP_485737    82 EKVFHNANFDVKLLGNKQAr----NITCTlEIAKKIPYYllpvqNYQLQSLAKLLCnfNNIDKQEQGSNWGQRPLSeEQI 157 Nostoc sp. PCC 7120
Feature 1        #   #                                              
1YT3_A      150 EYAAADVWYLLPITAKLMVEteas-------------gwlPAALDECRLMQM 188 Escherichia coli
NP_104433   150 EYAASDVLYLHRLRDVLAGRlare-------------grtKEADACFRFLPT 188 Mesorhizobium loti MAFF303099
YP_758935   148 QYAASDVLYLHQIKAGLEAMlere-------------grlELAQACFDFLPI 186 Hyphomonas neptunium ATCC 15444
NP_966626   149 SYAASDVLYLHRIKEKLDLMlere-------------nrkELAQKCFEFLPT 187 Wolbachia endosymbiont of Drosophila melanog...
NP_348532   152 QYATYDVIYLEKLWRALKAElika-------------nlySLAEECFKYLPT 190 Clostridium acetobutylicum ATCC 824
YP_872922   504 RYATNDVRYLPVLFDLLMNMarer-------------rleEAAMRRFRQMLK 542 Acidothermus cellulolyticus 11B
YP_265923   149 KYCANDVIYLHKIHEELNKIlvre-------------kriDLYKSCLAFLKT 187 Candidatus Pelagibacter ubique HTCC1062
YP_425107   151 TYAASDVLYLHALKARLDGLlare-------------grtTLAEGCFRFLPT 189 Rhodospirillum rubrum ATCC 11170
ZP_01631084 158 KYAAMDTVYLAAVHRKLLEIse-----------------pHAVANIFNMVNH 192 Nodularia spumigena CCY 9414
NP_485737   158 EYAYLDCIYLAQIHRRLLELqiesnpdpetlditvinsrfSQIEEQWKLLNS 209 Nostoc sp. PCC 7120

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