NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|85111309|ref|XP_963875|]
View 

hypothetical protein NCU08116 [Neurospora crassa OR74A]

Protein Classification

ribonuclease H family protein( domain architecture ID 54171)

ribonuclease H (RNase H) family protein may function as an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

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_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 172-350 4.48e-05

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; 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. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. 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 residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


The actual alignment was detected with superfamily member cd06222:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 121  Bit Score: 42.69  E-value: 4.48e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85111309 172 LFVDGSYQSPQnaepkilARGGYGVVFRNPYHGQgavefdhghsneswdntrpelntqeddlkrndfnIRSWSSH-RVYS 250
Cdd:cd06222   1 INVDGSCRGNP-------GPAGIGGVLRDHEGGW----------------------------------LGGFALKiGAPT 39

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85111309 251 SRHAEMAAVSQALEtvIAIVKRQQPssgvsVNIFSDCKDVINRiarrpvpesegMTDADALSMPLLRAIVWQSHYLFDEW 330
Cdd:cd06222  40 ALEAELLALLLALE--LALDLGYLK-----VIIESDSKYVVDL-----------INSGSFKWSPNILLIEDILLLLSRFW 101

                       170       180
                ....*....|....*....|.
gi 85111309 331 DCKVKlrWLPRCC-VLAHRLA 350
Cdd:cd06222 102 SVKIS--HVPREGnQVADALA 120
 
Name Accession Description Interval E-value
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 172-350 4.48e-05

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; 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. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. 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 residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 42.69  E-value: 4.48e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85111309 172 LFVDGSYQSPQnaepkilARGGYGVVFRNPYHGQgavefdhghsneswdntrpelntqeddlkrndfnIRSWSSH-RVYS 250
Cdd:cd06222   1 INVDGSCRGNP-------GPAGIGGVLRDHEGGW----------------------------------LGGFALKiGAPT 39

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85111309 251 SRHAEMAAVSQALEtvIAIVKRQQPssgvsVNIFSDCKDVINRiarrpvpesegMTDADALSMPLLRAIVWQSHYLFDEW 330
Cdd:cd06222  40 ALEAELLALLLALE--LALDLGYLK-----VIIESDSKYVVDL-----------INSGSFKWSPNILLIEDILLLLSRFW 101

                       170       180
                ....*....|....*....|.
gi 85111309 331 DCKVKlrWLPRCC-VLAHRLA 350
Cdd:cd06222 102 SVKIS--HVPREGnQVADALA 120
 
Name Accession Description Interval E-value
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 172-350 4.48e-05

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; 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. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. 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 residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 42.69  E-value: 4.48e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85111309 172 LFVDGSYQSPQnaepkilARGGYGVVFRNPYHGQgavefdhghsneswdntrpelntqeddlkrndfnIRSWSSH-RVYS 250
Cdd:cd06222   1 INVDGSCRGNP-------GPAGIGGVLRDHEGGW----------------------------------LGGFALKiGAPT 39

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85111309 251 SRHAEMAAVSQALEtvIAIVKRQQPssgvsVNIFSDCKDVINRiarrpvpesegMTDADALSMPLLRAIVWQSHYLFDEW 330
Cdd:cd06222  40 ALEAELLALLLALE--LALDLGYLK-----VIIESDSKYVVDL-----------INSGSFKWSPNILLIEDILLLLSRFW 101

                       170       180
                ....*....|....*....|.
gi 85111309 331 DCKVKlrWLPRCC-VLAHRLA 350
Cdd:cd06222 102 SVKIS--HVPREGnQVADALA 120
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 173-354 3.22e-03

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: 37.93  E-value: 3.22e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85111309 173 FVDGSYQSPQNAEpkilARGGYGVVFrnpyhgqgavefDHGHSneswdntrpelntqeddlkRNDfnirswsSHRVYSSR 252
Cdd:cd09280   3 YTDGSCLNNGKPG----ARAGIGVYF------------GPGDP-------------------RNV-------SEPLPGRK 40

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85111309 253 H----AEMAAVSQALETVIAIVKRQqpssgvsVNIFSDCKDVINRI-------ARRPVPESEGMTDADAlsmPLLRAIVw 321
Cdd:cd09280  41 QtnnrAELLAVIHALEQAPEEGIRK-------LEIRTDSKYAINCItkwipkwKKNGWKTSKGKPVKNQ---DLIKELD- 109

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 85111309 322 qshYLFDEWDCKVKLRWlprccVLAHR------LADHVA 354
Cdd:cd09280 110 ---KLLRKRGIKVKFEH-----VKGHSgdpgneEADRLA 140
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 254-354 4.45e-03

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: 37.20  E-value: 4.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85111309 254 AEMAAVSQALETVIAIVKRQQPssgvsVNIFSDCKDVINRIaRRPVPESegmtdadalSMPLLRAIVWQSHYLFDEwDCK 333
Cdd:cd09276  41 AELEAILEALELALATARRARK-----VTIFTDSQSALQAL-RNPRRSS---------GQVILIRILRLLRLLKAK-GVK 104

                        90       100
                ....*....|....*....|..
gi 85111309 334 VKLRWLPR-CCVLAHRLADHVA 354
Cdd:cd09276 105 VRLRWVPGhVGIEGNEAADRLA 126
 
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