NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1801179161|ref|WP_160840538|]
View 

MULTISPECIES: ribonuclease HI [Enterobacter]

Protein Classification

ribonuclease HI( domain architecture ID 10791836)

type 1 ribonuclease H is involved in the removal of RNA from RNA/DNA hybrids during DNA replication, repair and transcription

EC:  3.1.26.4
Gene Ontology:  GO:0004523

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
rnhA PRK00203
ribonuclease H; Reviewed
 39-188 6.92e-112

ribonuclease H; Reviewed


:

Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 315.23  E-value: 6.92e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  39 RKQVEIFTDGSCLGNPGPGGYGAIMRYRQHEKTFSEGYFLTTNNRMELMAAIVALEALKEHCDVVLSTDSQYVRQGITQW 118
Cdd:PRK00203    1 MKQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEW 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161 119 IHNWKKRGWKTAEKKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAASNPTHEDAGY 188
Cdd:PRK00203   81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEATLEDTGY 150
 
Name Accession Description Interval E-value
rnhA PRK00203
ribonuclease H; Reviewed
 39-188 6.92e-112

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 315.23  E-value: 6.92e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  39 RKQVEIFTDGSCLGNPGPGGYGAIMRYRQHEKTFSEGYFLTTNNRMELMAAIVALEALKEHCDVVLSTDSQYVRQGITQW 118
Cdd:PRK00203    1 MKQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEW 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161 119 IHNWKKRGWKTAEKKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAASNPTHEDAGY 188
Cdd:PRK00203   81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEATLEDTGY 150
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 41-178 3.21e-94

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: 270.12  E-value: 3.21e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  41 QVEIFTDGSCLGNPGPGGYGAIMRYRQHEKTFSEGYFLTTNNRMELMAAIVALEALKEHCDVVLSTDSQYVRQGITQWIH 120
Cdd:cd09278     1 EIVIYTDGACLGNPGPGGWAAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALKEPCPVTIYTDSQYVINGITKWIK 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1801179161 121 NWKKRGWKTAEKKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAA 178
Cdd:cd09278    81 GWKKNGWKTADGKPVKNRDLWQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAA 138
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
40-178 4.06e-81

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 237.05  E-value: 4.06e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  40 KQVEIFTDGSCLGNPGPGGYGAIMRYRQHEKTFSEGYFLTTNNRMELMAAIVALEALKEH--CDVVLSTDSQYVRQGITQ 117
Cdd:COG0328     1 KMIEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKELgpCEVEIYTDSQYVVNQITG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1801179161 118 WIHNWKKRGWktaekKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAA 178
Cdd:COG0328    81 WIHGWKKNGW-----KPVKNPDLWQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 39-179 2.52e-75

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: 222.64  E-value: 2.52e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  39 RKQVEIFTDGSCLGNPGPGGYGAIMrYRQHEkTFSEGYFL-TTNNRMELMAAIVALEALKEHCDVVLSTDSQYVRQGITQ 117
Cdd:pfam00075   1 PKAVTVYTDGSCLGNPGPGGAGAVL-YRGHE-NISAPLPGrTTNNRAELQAVIEALKALKSPSKVNIYTDSQYVIGGITQ 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1801179161 118 WIHNWKKRGWK-TAEKKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAAS 179
Cdd:pfam00075  79 WVHGWKKNGWPtTSEGKPVKNKDLWQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
 
Name Accession Description Interval E-value
rnhA PRK00203
ribonuclease H; Reviewed
 39-188 6.92e-112

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 315.23  E-value: 6.92e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  39 RKQVEIFTDGSCLGNPGPGGYGAIMRYRQHEKTFSEGYFLTTNNRMELMAAIVALEALKEHCDVVLSTDSQYVRQGITQW 118
Cdd:PRK00203    1 MKQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEW 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161 119 IHNWKKRGWKTAEKKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAASNPTHEDAGY 188
Cdd:PRK00203   81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEATLEDTGY 150
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 41-178 3.21e-94

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: 270.12  E-value: 3.21e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  41 QVEIFTDGSCLGNPGPGGYGAIMRYRQHEKTFSEGYFLTTNNRMELMAAIVALEALKEHCDVVLSTDSQYVRQGITQWIH 120
Cdd:cd09278     1 EIVIYTDGACLGNPGPGGWAAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALKEPCPVTIYTDSQYVINGITKWIK 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1801179161 121 NWKKRGWKTAEKKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAA 178
Cdd:cd09278    81 GWKKNGWKTADGKPVKNRDLWQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAA 138
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
40-178 4.06e-81

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 237.05  E-value: 4.06e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  40 KQVEIFTDGSCLGNPGPGGYGAIMRYRQHEKTFSEGYFLTTNNRMELMAAIVALEALKEH--CDVVLSTDSQYVRQGITQ 117
Cdd:COG0328     1 KMIEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKELgpCEVEIYTDSQYVVNQITG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1801179161 118 WIHNWKKRGWktaekKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAA 178
Cdd:COG0328    81 WIHGWKKNGW-----KPVKNPDLWQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 39-179 2.52e-75

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: 222.64  E-value: 2.52e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  39 RKQVEIFTDGSCLGNPGPGGYGAIMrYRQHEkTFSEGYFL-TTNNRMELMAAIVALEALKEHCDVVLSTDSQYVRQGITQ 117
Cdd:pfam00075   1 PKAVTVYTDGSCLGNPGPGGAGAVL-YRGHE-NISAPLPGrTTNNRAELQAVIEALKALKSPSKVNIYTDSQYVIGGITQ 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1801179161 118 WIHNWKKRGWK-TAEKKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAAS 179
Cdd:pfam00075  79 WVHGWKKNGWPtTSEGKPVKNKDLWQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 44-178 1.44e-48

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: 154.65  E-value: 1.44e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  44 IFTDGSCLGNPGPG---GYGAimrY--RQHEKTFSEGY--FLTTNNRMELMAAIVALEALKEHCD--VVLSTDSQYVRQG 114
Cdd:cd09280     2 VYTDGSCLNNGKPGaraGIGV---YfgPGDPRNVSEPLpgRKQTNNRAELLAVIHALEQAPEEGIrkLEIRTDSKYAINC 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1801179161 115 ITQWIHNWKKRGWKTAEKKPVKNVDLWKRLDAALGQHE--IKWEWVKGHAGHPENERCDELARAAA 178
Cdd:cd09280    79 ITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGikVKFEHVKGHSGDPGNEEADRLAREGA 144
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 44-178 2.67e-31

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: 111.14  E-value: 2.67e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  44 IFTDGSCLGNPGPG---GYGAIMRyrqHEKTFSEGYFLT-------TNNRMELMAAIVALEALKEHCD--------VVLS 105
Cdd:cd13934     2 VYIDGACRNNGRPDaraGYGVYFG---PDSSYNVSGRLEdtgghpqTSQRAELRAAIAALRFRSWIIDpdgeglktVVIA 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1801179161 106 TDSQYVRQGITQWIHNWKKRGWKTAEKKPVKNVDLWKRLDAALGQHE-----IKWEWVKGHaghpENERCDELARAAA 178
Cdd:cd13934    79 TDSEYVVKGATEWIPKWKRNGWRTSKGKPVKNRDLFELLLDEIEDLEeggveVQFWHVPRE----LNKEADRLAKAAA 152
PRK06548 PRK06548
ribonuclease H; Provisional
 46-180 2.08e-30

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 109.13  E-value: 2.08e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  46 TDGSCLGNPGPGGYGaimrYRQHEKTF-SEGYFLTTNNRMELMAAIVALEALKeHCD--VVLSTDSQYVRQGITQWIHNW 122
Cdd:PRK06548   10 TDGSSLANPGPSGWA----WYVDENTWdSGGWDIATNNIAELTAVRELLIATR-HTDrpILILSDSKYVINSLTKWVYSW 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1801179161 123 KKRGWKTAEKKPVKNVDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAAASN 180
Cdd:PRK06548   85 KMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQAANN 142
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 44-175 6.86e-23

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: 88.53  E-value: 6.86e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  44 IFTDGSCLGNPGPGGYGAIMRYRQHEKT--FSEGYFLTTNNRMELMAAIVALEALKEH--CDVVLSTDSQYVRQGITQWI 119
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVLRDHEGGWLggFALKIGAPTALEAELLALLLALELALDLgyLKVIIESDSKYVVDLINSGS 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1801179161 120 HNWKKrgwktaekkpvKNVDLWKRLDAALGQHEIKWEWVKGhaghPENERCDELAR 175
Cdd:cd06222    81 FKWSP-----------NILLIEDILLLLSRFWSVKISHVPR----EGNQVADALAK 121
PRK08719 PRK08719
ribonuclease H; Reviewed
 79-178 1.75e-22

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 88.38  E-value: 1.75e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  79 TTNNRMELMAAIVALEALKEHcDVVLStDSQYVRQGITQWIHNWKKRGWKTAEKKPVKNVDLWKRLDAALGQHEIKWEWV 158
Cdd:PRK08719   48 TDNAELELLALIEALEYARDG-DVIYS-DSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKV 125

                          90       100
                  ....*....|....*....|
gi 1801179161 159 KGHAGHPENERCDELARAAA 178
Cdd:PRK08719  126 TAHSGIEGNEAADMLAQAAA 145
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 42-179 1.67e-13

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: 64.03  E-value: 1.67e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  42 VEIFTDGSCLGNPGPGGYGAIMrYRQHEKTFSEGYFL---TTNNRMELMAAIVALEALKEH--CDVVLSTDSQYV-RQgi 115
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVI-YSPGGEVLELSERLgfpATNNEAEYEALIAGLELALELgaEKLEIYGDSQLVvNQ-- 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1801179161 116 tqwIH-NWKkrgwktaekkpVKNVDL---WKRLDAALGQHE-IKWEWVKGHaghpENERCDELARAAAS 179
Cdd:cd09279    78 ---LNgEYK-----------VKNERLkplLEKVLELLAKFElVELKWIPRE----QNKEADALANQALD 128
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 44-179 4.46e-13

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: 63.01  E-value: 4.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  44 IFTDGSclGNPGPGGYGAImrYRQHEKTFSEGYFLTTNNRM---ELMAAIVALEALKEHCD----VVLSTDSQYVRQGIT 116
Cdd:cd09276     2 IYTDGS--KLEGSVGAGFV--IYRGGEVISRSYRLGTHASVfdaELEAILEALELALATARrarkVTIFTDSQSALQALR 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1801179161 117 QWihnwkKRGWKTAEkkpvknVDLWKRLDAAL--GQHEIKWEWVKGHAGHPENERCDELARAAAS 179
Cdd:cd09276    78 NP-----RRSSGQVI------LIRILRLLRLLkaKGVKVRLRWVPGHVGIEGNEAADRLAKEAAS 131
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 42-177 3.57e-10

Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; 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 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. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids.


Pssm-ID: 260009 [Multi-domain]  Cd Length: 133  Bit Score: 55.57  E-value: 3.57e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  42 VEIFTDGSCLGNPGPGGYGAIMRYRQHEKTFSEGYFLTTNNRM-----ELMAAIVALEALKEH--CDVVLSTDsqYvrQG 114
Cdd:cd09277     1 VIAYVDGSYNKETKKYGYGVVIIKNGKEEEFSGSGNDPEYASMrnvagEIKGAMKAIKYAIENgiKKITIYYD--Y--EG 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1801179161 115 ITqwihNWKKRGWKTaeKKPVKNvDLWKRLDAALGQHEIKWEWVKGHAGHPENERCDELARAA 177
Cdd:cd09277    77 IE----KWATGEWKA--NKELTK-EYKEFMQKYKKKIKIEFVKVKAHSGDKYNELADKLAKKA 132
rnhA PRK13907
ribonuclease H; Provisional
 42-177 1.75e-08

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 50.82  E-value: 1.75e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  42 VEIFTDGSCLGNPGPGGYGAIMRYRQHEKTFSEGYFLTTNNRMELMAAIVALEALKEHCDVVLS--TDSQYVRQGItqwi 119
Cdd:PRK13907    2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSfrTDSQLVERAV---- 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1801179161 120 hnwkkrgwktaEKKPVKNVDLWKRLDAALgQHEIKWE-----WVKGhaghPENERCDELARAA 177
Cdd:PRK13907   78 -----------EKEYAKNKMFAPLLEEAL-QYIKSFDlffikWIPS----SQNKVADELARKA 124
RNase_H_bacteria_like cd13935
RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence ...
 47-161 2.90e-07

RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; This family includes bacterial ribonuclease H (RNase H) enzymes. RNases 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. 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260015  Cd Length: 133  Bit Score: 47.51  E-value: 2.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  47 DGSCLGNPGpggygaIMRYR-----QHEKTFSEGYF-LTTNNRMELMAAIVALEALKEH-CDVVLSTDSQYVRqgitQWI 119
Cdd:cd13935     8 DAACSGNPG------IVEYRgvdtkTGEVLFHRGPFpGGTNNMGEFLAIVHALRYLKEKnSRKPIYSDSQTAI----AWV 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1801179161 120 hnwKKRGWKTAEKKPVKNVDLWKRLDAALgqheikwEWVKGH 161
Cdd:cd13935    78 ---KKKKAKSTLVRNEKNAEIFKLVDRAE-------EWLSTH 109
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 38-192 2.85e-06

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 46.51  E-value: 2.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  38 MRKQVEifTDGSCLGNPGPGGYGAIMRYRQHEKTFSE-GYFL--TTNNRMELMAAIVALEALKE--HCDVVLSTDSQYVr 112
Cdd:PRK07238    1 MKVVVE--ADGGSRGNPGPAGYGAVVWDADRGEVLAErAEAIgrATNNVAEYRGLIAGLEAAAElgATEVEVRMDSKLV- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161 113 qgITQWIHNWKkrgwktaekkpVKNVDL------WKRLDAALGQheIKWEWV----KGHAGHPENERCDELARAAASNPT 182
Cdd:PRK07238   78 --VEQMSGRWK-----------VKHPDMkplaaqARELASQFGR--VTYTWIprarNAHADRLANEAMDAAAGGEPWGPS 142

                         170
                  ....*....|
gi 1801179161 183 HEDAGYQPES 192
Cdd:PRK07238  143 AAAADADPAK 152
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 43-120 7.98e-04

DIRS1 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. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 37.65  E-value: 7.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  43 EIFTDGSclGNpgpgGYGAIMRYRQHEKTFSEGYFLTTNNRMELMAAIVALEALKEH---CDVVLSTDS----QYV-RQG 114
Cdd:cd09275     1 VLFTDAS--LS----GWGAYLLNSRAHGPWSADERNKHINLLELKAVLLALQHFAAElknRKILIRTDNttavAYInKQG 74


                  ....*.
gi 1801179161 115 ITQWIH 120
Cdd:cd09275    75 GTSSPP 80
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 44-178 1.73e-03

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: 36.93  E-value: 1.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801179161  44 IFTDGSCLGNpgpgGYGAImryrqHEKTFSE---GYFLTTNNRMELMAAIVALEaLKEHCDVVLSTDSQYVRQGITQWIH 120
Cdd:cd09273     2 VFTDGSSFKA----GYAIV-----SGTEIVEaqpLPPGTSAQRAELIALIQALE-LAKGKPVNIYTDSAYAVHALHLLET 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1801179161 121 NWKKRGWktaeKKPVKNVDLWKRLDAALG-QHEIKWEWVKGHAGHPE-----NERCDELARAAA 178
Cdd:cd09273    72 IGIERGF----LKSIKNLSLFLQLLEAVQrPKPVAIIHIRAHSKLPGplaegNAQADAAAKQAA 131
 
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