Conserved Protein Domain Family
Rrp6p_like_exo

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cd06147: Rrp6p_like_exo 
Click on image for an interactive view with Cn3D
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins
Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain 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. The 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. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Statistics
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PSSM-Id: 99850
View PSSM: cd06147
Aligned: 28 rows
Threshold Bit Score: 298.743
Threshold Setting Gi: 71027523
Created: 26-Mar-2008
Updated: 17-Jan-2013
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:2HBL_A; Saccharomyces cerevisiae Rrp6p binds Mn and Zn in its catalytic site.
    View structure with Cn3D
  • Citation:PMID 9396823

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                     # #                                
2HBL_A        83 DDSVPIWVdtstELESMLEDLKN----------------TKEIAVDLEHHDyrsyyGIVCLMQISTRERDYLVDTLKLr- 145
gi 170575788 262 SDTELVYVdtleKLRSLRDVLNK----------------EQEFSVDLEHNAqrsflGLTCLMQISTRQMDYIIDPFPLw- 324
gi 118372761 240 LKEELVFVdkedILDEMIESLKQ----------------CSEVAIDLEHHSyrsfnGITCLMQISSRTKDYIVDVFSVw- 302
gi 145548742 188 DLEPPMMItnadHLGELVLKIQQevd----------qngFSEIAVDLEHNHqisylGITCLIQLSTRSQDYIIDPFPLwk 257
gi 156083893 312 SCKRCKLVqtleELESMITLLKK----------------CSIVAIDVEHHStqsyrGFVCLVQITGADDDWVIDPFSIf- 374
gi 17531757  274 KDTPLTMIdtkeKLEALTKTLNS----------------VKEFAVDLEHHQmrsylGLTCLIQISTRDEDFIIDPFPIw- 336
gi 162693577  62 MEGPCLWVqtrsQLEALVDVLKG----------------EKEIGVDIEHHHvrsfrGFIPLIQISTYSTDYLVDAIALh- 124
gi 72387778  242 VTCPLTFVdtveDLEALVAVLLN----------------ETEIAVDLEHHDfysyqGFTCLMQISTRTQDFIVDCLKVr- 304
gi 169802269 183 EKTPLIYVntleLLQEMIVSLNH----------------VNQFAVDVEHHSehsyyGFVCLLQISTRSSDYIIDTITLr- 245
gi 66357594  262 SNTPLTFIkepgDLRRMIDDILNlmeshysqssmneessPFLLAIDVEHHSnqsykGFVSLIQLSTRTHDYIIDPFNLf- 340
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                #                                                       
2HBL_A       146 eNLHILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLp-RHSLAYLLENFAnFKTSKKYQLADWR 224
gi 170575788 325 nDMHILNEPFTDPNILKVFHGADSDIVWLQRDFGIYVVNMFDTYKAMRVLNFs-KFSYQHLVQTCCnHTLDKKFQKADWR 403
gi 118372761 303 kSLHKLNAVTTDKNIVKVLHGADMDIQWLQRDFGIYIVNLFDTGQAARTLSMp-SYALAYLLQSISkVPTDKKYQLADWR 381
gi 145548742 258 qLGDMLSVIFANPKIVKVFHGAENDVQWLQRDFGLYIVNLFDTFHASKELQLm-QNSFQFLLSEYCkKSTDKTYQTADWT 336
gi 156083893 375 dEMWRLNDVTTDPRILKVMHGAESDILWLQRDFGVYVVNLFDTLKAADVLCLscGHSLSSLVRHFLgIHLDKSYQLADWR 454
gi 17531757  337 dHVGMLNEPFANPRILKVFHGSDSDVLWLQRDYGVHVVNLFDTYVAMKKLKYp-KFSLAYLTLRFAdVVLDKQYQLADWR 415
gi 162693577 125 dDMHLLHPIFANPAILKIFHGADNDSLWLQRDFHIYIVNLFDTARACDVLGKp-QRSLAYLLQLYCgVSTKKIYQRSDWR 203
gi 72387778  305 aNMYLMAPVFLQPNIVKVFHGAREDVRWLQKDFGLYIVNLFDTSIALQNLHM--PHSLAFAVDHFCqVKLNKKYQTADWR 382
gi 169802269 246 dSITLLNDPFTNPNIEKVFHGCDFDMIWLSYNFGLYVVNCIDSGQCARALKLq-HFSLKYLLQKYCnVDADKKYQLADWR 324
gi 66357594  341 nEIQMLNELTANPKILKVLHGSDYDIIWLQRDFSVYIVNMFDTGQAARILNTpgGYSLKNLLSIYCsLDIDKRFQLADWR 420
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
Feature 1                  #   #                                      
2HBL_A       225 IRPLSKPMTAAARADTHFLLNIYDQLRNKLies----nklAGVLYESRNVAKR 273
gi 170575788 404 LRPLTIAHKTYARSDTHYLLHCYDQLRKRLlsq----enaANNLLEFVYNESA 452
gi 118372761 382 IRPLPREMISYARSDTHYLLSIYDNLRIQLvskalqqgqnASHFIESVLNKSR 434
gi 145548742 337 QRPLPDEMIKYAQIDTHYLLYIYDRMRQDLkkl----nkpNDNISNIPNYYLE 385
gi 156083893 455 IRPIPRDMLTYATADTHYLLDLYSALKNTAleqd--lkynIPGMVGCFDNHIW 505
gi 17531757  416 ARPLRNAMINYAREDTHYLLYSYDMLREQLlkqd--tkdlANVYSESSDLCIK 466
gi 162693577 204 VRPLPAEMEIYARTDAHYLLYIAQCMRANLv---------QACNTPSLLNDNQ 247
gi 72387778  383 VRPIPAEMVSYAQQDTHFLLYVYDRLKQLLlnce--arasVGNMLLHVFQESR 433
gi 169802269 325 LRPLTKEMIEYARGDTHYLLYIIDQLRNECida----gvlEEVLNKSNELCLR 373
gi 66357594  421 ERPLSNELIEYARGDTHYLLYIYDIMKNLLll-------hRHKNTEPPVLASD 466

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