2HBL,2HBJ


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: 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: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:
Feature 1                                                     # #                                
2HBL_A        83 DDSVPIWVdtstELESMLEDLKN----------------TKEIAVDLEHHDyrsyyGIVCLMQISTRERDYLVDTLKLr- 145  baker's yeast
XP_001893385 262 SDTELVYVdtleKLRSLRDVLNK----------------EQEFSVDLEHNAqrsflGLTCLMQISTRQMDYIIDPFPLw- 324  agent of lymph...
XP_001019575 240 LKEELVFVdkedILDEMIESLKQ----------------CSEVAIDLEHHSyrsfnGITCLMQISSRTKDYIVDVFSVw- 302  Tetrahymena th...
XP_001460051 188 DLEPPMMItnadHLGELVLKIQQevd----------qngFSEIAVDLEHNHqisylGITCLIQLSTRSQDYIIDPFPLwk 257  Paramecium tet...
XP_001609430 312 SCKRCKLVqtleELESMITLLKK----------------CSIVAIDVEHHStqsyrGFVCLVQITGADDDWVIDPFSIf- 374  Babesia bovis ...
NP_496283    274 KDTPLTMIdtkeKLEALTKTLNS----------------VKEFAVDLEHHQmrsylGLTCLIQISTRDEDFIIDPFPIw- 336  nematode
EDQ79929      62 MEGPCLWVqtrsQLEALVDVLKG----------------EKEIGVDIEHHHvrsfrGFIPLIQISTYSTDYLVDAIALh- 124  Physcomitrella...
XP_844313    242 VTCPLTFVdtveDLEALVAVLLN----------------ETEIAVDLEHHDfysyqGFTCLMQISTRTQDFIVDCLKVr- 304  Trypanosoma br...
EAL45368     183 EKTPLIYVntleLLQEMIVSLNH----------------VNQFAVDVEHHSehsyyGFVCLLQISTRSSDYIIDTITLr- 245  Entamoeba hist...
XP_625975    262 SNTPLTFIkepgDLRRMIDDILNlmeshysqssmneessPFLLAIDVEHHSnqsykGFVSLIQLSTRTHDYIIDPFNLf- 340  Cryptosporidiu...
Feature 1                                #                                                       
2HBL_A       146 eNLHILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLp-RHSLAYLLENFAnFKTSKKYQLADWR 224  baker's yeast
XP_001893385 325 nDMHILNEPFTDPNILKVFHGADSDIVWLQRDFGIYVVNMFDTYKAMRVLNFs-KFSYQHLVQTCCnHTLDKKFQKADWR 403  agent of lymph...
XP_001019575 303 kSLHKLNAVTTDKNIVKVLHGADMDIQWLQRDFGIYIVNLFDTGQAARTLSMp-SYALAYLLQSISkVPTDKKYQLADWR 381  Tetrahymena th...
XP_001460051 258 qLGDMLSVIFANPKIVKVFHGAENDVQWLQRDFGLYIVNLFDTFHASKELQLm-QNSFQFLLSEYCkKSTDKTYQTADWT 336  Paramecium tet...
XP_001609430 375 dEMWRLNDVTTDPRILKVMHGAESDILWLQRDFGVYVVNLFDTLKAADVLCLscGHSLSSLVRHFLgIHLDKSYQLADWR 454  Babesia bovis ...
NP_496283    337 dHVGMLNEPFANPRILKVFHGSDSDVLWLQRDYGVHVVNLFDTYVAMKKLKYp-KFSLAYLTLRFAdVVLDKQYQLADWR 415  nematode
EDQ79929     125 dDMHLLHPIFANPAILKIFHGADNDSLWLQRDFHIYIVNLFDTARACDVLGKp-QRSLAYLLQLYCgVSTKKIYQRSDWR 203  Physcomitrella...
XP_844313    305 aNMYLMAPVFLQPNIVKVFHGAREDVRWLQKDFGLYIVNLFDTSIALQNLHM--PHSLAFAVDHFCqVKLNKKYQTADWR 382  Trypanosoma br...
EAL45368     246 dSITLLNDPFTNPNIEKVFHGCDFDMIWLSYNFGLYVVNCIDSGQCARALKLq-HFSLKYLLQKYCnVDADKKYQLADWR 324  Entamoeba hist...
XP_625975    341 nEIQMLNELTANPKILKVLHGSDYDIIWLQRDFSVYIVNMFDTGQAARILNTpgGYSLKNLLSIYCsLDIDKRFQLADWR 420  Cryptosporidiu...
Feature 1                  #   #                                      
2HBL_A       225 IRPLSKPMTAAARADTHFLLNIYDQLRNKLies----nklAGVLYESRNVAKR 273  baker's yeast
XP_001893385 404 LRPLTIAHKTYARSDTHYLLHCYDQLRKRLlsq----enaANNLLEFVYNESA 452  agent of lymphatic filariasis
XP_001019575 382 IRPLPREMISYARSDTHYLLSIYDNLRIQLvskalqqgqnASHFIESVLNKSR 434  Tetrahymena thermophila SB210
XP_001460051 337 QRPLPDEMIKYAQIDTHYLLYIYDRMRQDLkkl----nkpNDNISNIPNYYLE 385  Paramecium tetraurelia strain d4-2
XP_001609430 455 IRPIPRDMLTYATADTHYLLDLYSALKNTAleqd--lkynIPGMVGCFDNHIW 505  Babesia bovis T2Bo
NP_496283    416 ARPLRNAMINYAREDTHYLLYSYDMLREQLlkqd--tkdlANVYSESSDLCIK 466  nematode
EDQ79929     204 VRPLPAEMEIYARTDAHYLLYIAQCMRANLv---------QACNTPSLLNDNQ 247  Physcomitrella patens subsp. patens
XP_844313    383 VRPIPAEMVSYAQQDTHFLLYVYDRLKQLLlnce--arasVGNMLLHVFQESR 433  Trypanosoma brucei TREU927
EAL45368     325 LRPLTKEMIEYARGDTHYLLYIIDQLRNECida----gvlEEVLNKSNELCLR 373  Entamoeba histolytica HM-1:IMSS
XP_625975    421 ERPLSNELIEYARGDTHYLLYIYDIMKNLLll-------hRHKNTEPPVLASD 466  Cryptosporidium parvum Iowa II

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