Conserved Protein Domain Family
RNase_HI_RT_Ty3

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cd09274: RNase_HI_RT_Ty3 
Ty3/Gypsy family of RNase HI in long-term repeat retroelements
Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Statistics
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PSSM-Id: 260006
Aligned: 313 rows
Threshold Bit Score: 101.415
Threshold Setting Gi: 90265044
Created: 15-Jun-2010
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
active siteRNA/DNA hybrid
Feature 1: active site [active site], 4 residue positions
Conserved feature residue pattern:D E D DClick to see conserved feature residue pattern help
Evidence:
  • Comment:Based on homology to RNase HI structures.
  • Comment:The four conserved carboxylates are directly involved in coordinating the metal ions.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1          #                                            #                        #     
ABA91843   836 TIEADACGtGIGAVLMQg--------DRPIAFYSKSLGPkaaaqSIYEKEAMAILEALKKWRHYFlGSKLVIKTDQ---Q 904  Japanese rice
ABL86690   655 ILTTDASGiGIGGVLQQevd----gqLHNLYYHSQVLTPcekrySTIEKEALAIYKCFVRMRPFLlGREITIMTDH---C 727  Philodina roseola
AAM43937   617 IIFTDASHmVVGGYLCQptfrndkevLVPIAFSSHKLTEtqsryAAMEKELLAIIVILEKFRYHC-SNTVEIYTDH---Q 692  Candida albicans
EFA13184     2 RVTNRCLSrQFRSFLLQkcd----gqLHLIAYTSCTLSKskknySITELEALAGIYGLTHFQHFIhGRPVTIKSDH---Q 74   red flour beetle
EDO18103  1044 IIYTDASLtGAASILLQpenqngntiLYPIAFYSIRFNPtqqrySTVERELWAVLHTLEKARLLL-SSNITIYTDN---Q 1119 Vanderwaltozyma ...
XP_719902   20 LVFTDASQlAIGAIITQehliqgqksLVPVAMVSLRLSAtqqrySTLERELLTIVYVLQKYKQFM-SREVQFYTDH---Q 95   Candida albicans...
ABD63139   980 LLYVRAMEhSLGALLAQnnd---qgqEQAVYYLSRTMMGaehryNPVEKECLALVFAVQKMRHYLvGQTIYVISKV---N 1053 garden asparagus
CAN69610  1339 LLYLSVSDmALGCMLAQldd---lgkERAIYYLSKRMLEyeckyIMIERLCLAVVWATRRLRHYMtEYSVLLVSRL---D 1412 wine grape
AAF79618  1122 YLYIAVSDhAVSSVLVRedr----geQRPIFYTSKSLVEaetryPVIEKAALAVVTSARKLRPYFqSHTIAVLTDQplrV 1197 thale cress
AAR06327   698 RLYLSASGkSIGSVLIQele----gkERVVFYLSRQLLDaetiySPVEKLCLCLYFSCTRFRHYLlSNECTVICKA---N 770  Japanese rice
Feature 1                                                     #      
ABA91843   905 SLKHMMnqrl-vegIQHKLLLKLm-eYDYIIEYKAGk-----dNVVADALSRLP 951  Japanese rice
ABL86690   728 PLCHIMtktv-nnsRVDRIATLIqeyNINKVVHIDGr-----qNCLPDYLSRYP 775  Philodina roseola
AAM43937   693 SLASFLdkkttpppRIARFLDLIg-sFSPKVYYLSGk-----kNFVADIITRYQ 740  Candida albicans
EFA13184    75 TLCYLKntnq-ttgRLTRWVIKLq-eFHYEIVFKNGk-----aHKHVDYLSRNP 121  red flour beetle
EDO18103  1120 GIISIGkterathpRLTKYLDLLn-tYRLTWKYIKGs-----qNYVADYLSRYG 1167 Vanderwaltozyma polyspora DSM 70294
XP_719902   96 AITTIGsaksepanRIKRFIDIIq-sFNPSIYFIPGq-----fNFIADFLSRYN 143  Candida albicans SC5314
ABD63139  1054 PLRVLMtkpsslncRLAKWAILLs-qYDMQFMPQKAvk----gQALADFLADHP 1102 garden asparagus
CAN69610  1413 PLRYLFdrpv-ltgRLMRWLVLLt-eFDIHYVTQKSik----gSIVADHLASLP 1460 wine grape
AAF79618  1198 ALHSPSqs-----gRMTKWAVELs-eYDIDFRPRPAmk----sQVLADFLIELP 1241 thale cress
AAR06327   771 VVKYMLsapi-lkgRVGKWIFSLt-eFDLRYESPKAvkgqaivNFIVDHRDNSI 822  Japanese rice

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