NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2103706262|ref|XP_043862431|]
View 

uncharacterized protein LOC122756531 [Drosophila santomea]

Protein Classification

ribonuclease H family protein( domain architecture ID 10174525)

ribonuclease H (RNaseH) family protein containing a reverse transcriptase (RT)-like domain, may be an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

EC:  3.1.26.4
Gene Ontology:  GO:0003723|GO:0004540
PubMed:  16093691

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 249-350 1.01e-26

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, 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. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 104.61  E-value: 1.01e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2103706262 249 NIYTDGSKMEGGVGAGIYCTDP--EMRLSYKLPSQCSIFQAEVFAIG----------------------QAAIRSMQSSA 304
Cdd:cd09276     1 VIYTDGSKLEGSVGAGFVIYRGgeVISRSYRLGTHASVFDAELEAILealelalatarrarkvtiftdsQSALQALRNPR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2103706262 305 VSSKSVLASREALDI----STTTSVRIYWVPSHQGIDGIETADGLAKEGV 350
Cdd:cd09276    81 RSSGQVILIRILRLLrllkAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
 
Name Accession Description Interval E-value
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 249-350 1.01e-26

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, 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. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 104.61  E-value: 1.01e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2103706262 249 NIYTDGSKMEGGVGAGIYCTDP--EMRLSYKLPSQCSIFQAEVFAIG----------------------QAAIRSMQSSA 304
Cdd:cd09276     1 VIYTDGSKLEGSVGAGFVIYRGgeVISRSYRLGTHASVFDAELEAILealelalatarrarkvtiftdsQSALQALRNPR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2103706262 305 VSSKSVLASREALDI----STTTSVRIYWVPSHQGIDGIETADGLAKEGV 350
Cdd:cd09276    81 RSSGQVILIRILRLLrllkAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
247-350 2.36e-03

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 38.29  E-value: 2.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2103706262 247 HFNIYTDGSKM----EGGVGAGIYCTDPEMRLSYKLPSQCSIfQAEVFAIGQA--AIRSMQSSAVS----SKSVLAS--- 313
Cdd:COG0328     2 MIEIYTDGACRgnpgPGGWGAVIRYGGEEKELSGGLGDTTNN-RAELTALIAAleALKELGPCEVEiytdSQYVVNQitg 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2103706262 314 -------------------REALDISTTTSVRIYWVPSHQGIDGIETADGLAKEGV 350
Cdd:COG0328    81 wihgwkkngwkpvknpdlwQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
 
Name Accession Description Interval E-value
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 249-350 1.01e-26

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, 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. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 104.61  E-value: 1.01e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2103706262 249 NIYTDGSKMEGGVGAGIYCTDP--EMRLSYKLPSQCSIFQAEVFAIG----------------------QAAIRSMQSSA 304
Cdd:cd09276     1 VIYTDGSKLEGSVGAGFVIYRGgeVISRSYRLGTHASVFDAELEAILealelalatarrarkvtiftdsQSALQALRNPR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2103706262 305 VSSKSVLASREALDI----STTTSVRIYWVPSHQGIDGIETADGLAKEGV 350
Cdd:cd09276    81 RSSGQVILIRILRLLrllkAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 324-349 1.99e-04

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 41.40  E-value: 1.99e-04
                          10        20
                  ....*....|....*....|....*.
gi 2103706262 324 SVRIYWVPSHQGIDGIETADGLAKEG 349
Cdd:cd09280   118 KVKFEHVKGHSGDPGNEEADRLAREG 143
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
247-350 2.36e-03

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 38.29  E-value: 2.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2103706262 247 HFNIYTDGSKM----EGGVGAGIYCTDPEMRLSYKLPSQCSIfQAEVFAIGQA--AIRSMQSSAVS----SKSVLAS--- 313
Cdd:COG0328     2 MIEIYTDGACRgnpgPGGWGAVIRYGGEEKELSGGLGDTTNN-RAELTALIAAleALKELGPCEVEiytdSQYVVNQitg 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2103706262 314 -------------------REALDISTTTSVRIYWVPSHQGIDGIETADGLAKEGV 350
Cdd:COG0328    81 wihgwkkngwkpvknpdlwQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH