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Conserved domains on  [gi|329666228]
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Chain A, Gag-Pol polyprotein,Ribonuclease HI,Gag-Pol polyprotein

Protein Classification

ribonuclease H family protein( domain architecture ID 10442158)

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

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List of domain hits

 Name Accession Description Interval E-value
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 12-146 4.65e-53

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


:

Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 164.47  E-value: 4.65e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228   12 AETFYVDGAANRETKLGKAGYVTNRGRQ--KVVTLTDTTNQKTELQAIYLALQD--SGLEVNIVTDSQYALGIITQWIHN 87
Cdd:pfam00075   3 AVTVYTDGSCLGNPGPGGAGAVLYRGHEniSAPLPGRTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGITQWVHG 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228   88 WKKRGWKTADK-KPVKNVDLVnQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 146
Cdd:pfam00075  83 WKKNGWPTTSEgKPVKNKDLW-QLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
 
Name Accession Description Interval E-value
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 12-146 4.65e-53

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 164.47  E-value: 4.65e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228   12 AETFYVDGAANRETKLGKAGYVTNRGRQ--KVVTLTDTTNQKTELQAIYLALQD--SGLEVNIVTDSQYALGIITQWIHN 87
Cdd:pfam00075   3 AVTVYTDGSCLGNPGPGGAGAVLYRGHEniSAPLPGRTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGITQWVHG 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228   88 WKKRGWKTADK-KPVKNVDLVnQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 146
Cdd:pfam00075  83 WKKNGWPTTSEgKPVKNKDLW-QLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 16-146 1.01e-34

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 117.58  E-value: 1.01e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  16 YVDGAANRETklGKAGY-VTNRGRQKVVTLT----DTTNQKTELQAIYLALQ--DSGLEVNIVTDSQYALGIITQWIHNW 88
Cdd:cd09278    5 YTDGACLGNP--GPGGWaAVIRYGDHEKELSggepGTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVINGITKWIKGW 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 329666228  89 KKRGWKTADKKPVKNVDLVnQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 146
Cdd:cd09278   83 KKNGWKTADGKPVKNRDLW-QELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
rnhA PRK00203
ribonuclease H; Reviewed
 46-149 1.25e-31

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 110.30  E-value: 1.25e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  46 DTTNQKTELQAIYLALQ--DSGLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVnQIIEQLIKKEKVYLA 123
Cdd:PRK00203  40 LTTNNRMELMAAIEALEalKEPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLW-QRLDAALKRHQIKWH 118

                         90       100
                 ....*....|....*....|....*.
gi 329666228 124 WVPAHKGIGGNEQVDKLVSAGIRKVL 149
Cdd:PRK00203 119 WVKGHAGHPENERCDELARAGAEEAT 144
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
16-145 7.45e-31

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 107.62  E-value: 7.45e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  16 YVDGAANRETKLGKAGYV---TNRGRQKVVTLTDTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIITQWIHNW 88
Cdd:COG0328    6 YTDGACRGNPGPGGWGAViryGGEEKELSGGLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITGWIHGW 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 329666228  89 KKRGWktadkKPVKNVDLVNQIIEqLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI 145
Cdd:COG0328   86 KKNGW-----KPVKNPDLWQRLDE-LLARHKVTFEWVKGHAGHPGNERADALANKAL 136
 
Name Accession Description Interval E-value
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 12-146 4.65e-53

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 164.47  E-value: 4.65e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228   12 AETFYVDGAANRETKLGKAGYVTNRGRQ--KVVTLTDTTNQKTELQAIYLALQD--SGLEVNIVTDSQYALGIITQWIHN 87
Cdd:pfam00075   3 AVTVYTDGSCLGNPGPGGAGAVLYRGHEniSAPLPGRTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGITQWVHG 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228   88 WKKRGWKTADK-KPVKNVDLVnQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 146
Cdd:pfam00075  83 WKKNGWPTTSEgKPVKNKDLW-QLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 16-146 1.01e-34

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 117.58  E-value: 1.01e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  16 YVDGAANRETklGKAGY-VTNRGRQKVVTLT----DTTNQKTELQAIYLALQ--DSGLEVNIVTDSQYALGIITQWIHNW 88
Cdd:cd09278    5 YTDGACLGNP--GPGGWaAVIRYGDHEKELSggepGTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVINGITKWIKGW 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 329666228  89 KKRGWKTADKKPVKNVDLVnQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 146
Cdd:cd09278   83 KKNGWKTADGKPVKNRDLW-QELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 16-146 3.00e-32

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: 111.50  E-value: 3.00e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  16 YVDGAA-NRETKLGKAGYV------TNRGRQKVVTLTDTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIITQW 84
Cdd:cd09280    3 YTDGSClNNGKPGARAGIGvyfgpgDPRNVSEPLPGRKQTNNRAELLAVIHALEqapeEGIRKLEIRTDSKYAINCITKW 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 329666228  85 IHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKLVSAGIR 146
Cdd:cd09280   83 IPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGiKVKFEHVKGHSGDPGNEEADRLAREGAD 145
rnhA PRK00203
ribonuclease H; Reviewed
 46-149 1.25e-31

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 110.30  E-value: 1.25e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  46 DTTNQKTELQAIYLALQ--DSGLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVnQIIEQLIKKEKVYLA 123
Cdd:PRK00203  40 LTTNNRMELMAAIEALEalKEPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLW-QRLDAALKRHQIKWH 118

                         90       100
                 ....*....|....*....|....*.
gi 329666228 124 WVPAHKGIGGNEQVDKLVSAGIRKVL 149
Cdd:PRK00203 119 WVKGHAGHPENERCDELARAGAEEAT 144
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
16-145 7.45e-31

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 107.62  E-value: 7.45e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  16 YVDGAANRETKLGKAGYV---TNRGRQKVVTLTDTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIITQWIHNW 88
Cdd:COG0328    6 YTDGACRGNPGPGGWGAViryGGEEKELSGGLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITGWIHGW 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 329666228  89 KKRGWktadkKPVKNVDLVNQIIEqLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI 145
Cdd:COG0328   86 KKNGW-----KPVKNPDLWQRLDE-LLARHKVTFEWVKGHAGHPGNERADALANKAL 136
PRK08719 PRK08719
ribonuclease H; Reviewed
 14-147 7.25e-20

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 79.90  E-value: 7.25e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  14 TFYVDGAA-NRETKLGKAGY---VTNRGRQKVVTLT-----DTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIITQW 84
Cdd:PRK08719   6 SIYIDGAApNNQHGCVRGGIglvVYDEAGEIVDEQSitvnrYTDNAELELLALIEALEYARDGDVIYSDSDYCVRGFNEW 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 329666228  85 IHNWKKRGWKTADKKPVKNVDLVNQiIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK 147
Cdd:PRK08719  86 LDTWKQKGWRKSDKKPVANRDLWQQ-VDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAEL 147
PRK06548 PRK06548
ribonuclease H; Provisional
 48-140 2.20e-16

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 71.38  E-value: 2.20e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  48 TNQKTELQAI---YLALQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVnQIIEQLIKKEKVYLAW 124
Cdd:PRK06548  41 TNNIAELTAVrelLIATRHTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEII-QEIDSLMENRNIRMSW 119

                         90
                 ....*....|....*.
gi 329666228 125 VPAHKGIGGNEQVDKL 140
Cdd:PRK06548 120 VNAHTGHPLNEAADSL 135
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 14-141 1.39e-13

Bel/Pao 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 eukaryote. 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. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 63.13  E-value: 1.39e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  14 TFYVDGAAnreTKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD-SGLEVNIVTDSQYALGIITQWIHNWKKRG 92
Cdd:cd09273    1 TVFTDGSS---FKAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELaKGKPVNIYTDSAYAVHALHLLETIGIERG 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 329666228  93 WktadKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIG-----GNEQVDKLV 141
Cdd:cd09273   78 F----LKSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPgplaeGNAQADAAA 127
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 15-114 1.62e-13

Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. 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.


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 63.76  E-value: 1.62e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  15 FYVDGAANRETKLG-KAGY-----VTNRGRQKVVtLTDT-----TNQKTELQAIYLALQ---------DSGLE-VNIVTD 73
Cdd:cd13934    2 VYIDGACRNNGRPDaRAGYgvyfgPDSSYNVSGR-LEDTgghpqTSQRAELRAAIAALRfrswiidpdGEGLKtVVIATD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 329666228  74 SQYALGIITQWIHNWKKRGWKTADKKPVKNVDL---VNQIIEQL 114
Cdd:cd13934   81 SEYVVKGATEWIPKWKRNGWRTSKGKPVKNRDLfelLLDEIEDL 124
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 14-146 3.51e-11

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: 56.84  E-value: 3.51e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  14 TFYVDGAANrETKLGkAGYVTNRGRQKVVTLTDTTNQKT----ELQAIYLALQ------DSGLEVNIVTDSQYALgiitQ 83
Cdd:cd09276    1 VIYTDGSKL-EGSVG-AGFVIYRGGEVISRSYRLGTHASvfdaELEAILEALElalataRRARKVTIFTDSQSAL----Q 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 329666228  84 WIHNWKKRgwktadKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 146
Cdd:cd09276   75 ALRNPRRS------SGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAAS 131
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 16-140 1.50e-08

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: 50.01  E-value: 1.50e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  16 YVDGAANRETKLGKAGYVtNRGRQKVVTLTDT------TNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIITQWI 85
Cdd:cd06222    2 NVDGSCRGNPGPAGIGGV-LRDHEGGWLGGFAlkigapTALEAELLALLLALElaldLGYLKVIIESDSKYVVDLINSGS 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 329666228  86 HNWKkrgwktadkkpvKNVDLVNQIIEQLIKKEKVYLAWVPAHkgigGNEQVDKL 140
Cdd:cd06222   81 FKWS------------PNILLIEDILLLLSRFWSVKISHVPRE----GNQVADAL 119
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 16-146 5.98e-04

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 37.45  E-value: 5.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 329666228  16 YVDGAANRETKLGKAGYV----TNRGRQKVVTLT-DTTNQKTELQAIYLALQ---DSGLE-VNIVTDSQyalgIITQWIH 86
Cdd:cd09279    4 YFDGASRGNPGPAGAGVViyspGGEVLELSERLGfPATNNEAEYEALIAGLElalELGAEkLEIYGDSQ----LVVNQLN 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 329666228  87 -NWKkrgwktadkkpVKNVDL---VNQIIEQLIKKEKVYLAWVPAHKgiggNEQVDKLVSAGIR 146
Cdd:cd09279   80 gEYK-----------VKNERLkplLEKVLELLAKFELVELKWIPREQ----NKEADALANQALD 128
 
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.
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