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Conserved domains on  [gi|30695999|ref|NP_199921|]
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RNase H family protein [Arabidopsis thaliana]

Protein Classification

ribonuclease HI family protein( domain architecture ID 10174584)

ribonuclease HI family protein such as type 1 ribonuclease H, which is involved in the removal of RNA from RNA/DNA hybrids during DNA replication, repair and transcription; similar to Enterococcus faecalis hydrolase EbsB

CATH:  3.30.420.10
EC:  3.-.-.-
Gene Ontology:  GO:0004523|GO:0003676|GO:0000287|GO:0043137
PubMed:  19228198|19228197|16093691|16232566|2177653
SCOP:  4000541

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 186-313 4.36e-47

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: 154.94  E-value: 4.36e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999 186 CIIEFDGASKGNPGLSGAAAVLKTEDGsLIFKMRQGLGI-ATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMK 264
Cdd:cd09279   1 WTLYFDGASRGNPGPAGAGVVIYSPGG-EVLELSERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 30695999 265 GQWKVNHEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMAAR 313
Cdd:cd09279  80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
 
Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 186-313 4.36e-47

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: 154.94  E-value: 4.36e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999 186 CIIEFDGASKGNPGLSGAAAVLKTEDGsLIFKMRQGLGI-ATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMK 264
Cdd:cd09279   1 WTLYFDGASRGNPGPAGAGVVIYSPGG-EVLELSERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 30695999 265 GQWKVNHEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMAAR 313
Cdd:cd09279  80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 187-311 1.46e-33

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 126.63  E-value: 1.46e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999  187 IIEFDGASKGNPGLSGAAAVLKTEDGSLIFKMR-QGLGIATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMKG 265
Cdd:PRK07238   4 VVEADGGSRGNPGPAGYGAVVWDADRGEVLAERaEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSG 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 30695999  266 QWKVNHEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMA 311
Cdd:PRK07238  84 RWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA 129
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
187-312 4.33e-29

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 108.39  E-value: 4.33e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999 187 IIEFDGASKGNPGLSGAAAVLKteDGSLIFKMRQGLGIATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMKG- 265
Cdd:COG0328   4 EIYTDGACRGNPGPGGWGAVIR--YGGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGw 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30695999 266 --QWKVNH--EVLSK-LHKEAKQLSDKClSFEISHVLRS----LNSDADEQANMAA 312
Cdd:COG0328  82 ihGWKKNGwkPVKNPdLWQRLDELLARH-KVTFEWVKGHaghpGNERADALANKAL 136
RNAseHI_Thmprot NF041175
ribonuclease HI;
186-314 1.65e-22

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 91.18  E-value: 1.65e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999  186 CIIEFDGASK-GNPGlsGAAA---VLKTEDGSLIfkmrQGLGIA--------TNNAAEYHGLILGLKHAIEKGYTKIKVK 253
Cdd:NF041175   2 AIGYFDGLCEpKNPG--GIATygyVIYLDNKRKI----EGYGLAaepwskdsTNNVAEYTGLICLLEKLLELGISEVIIR 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30695999  254 TDSKLVCMQMKGQWKVNHEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMAARL 314
Cdd:NF041175  76 GDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRIAYEL 136
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 190-311 1.91e-21

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 87.71  E-value: 1.91e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999   190 FDGASKGNPGLSGAAAVLKTEDGSLIFKM-RQGLGIATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMKGQWK 268
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVLLAGqKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSP 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 30695999   269 vNHEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMA 311
Cdd:pfam13456  82 -KQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
 
Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 186-313 4.36e-47

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: 154.94  E-value: 4.36e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999 186 CIIEFDGASKGNPGLSGAAAVLKTEDGsLIFKMRQGLGI-ATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMK 264
Cdd:cd09279   1 WTLYFDGASRGNPGPAGAGVVIYSPGG-EVLELSERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 30695999 265 GQWKVNHEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMAAR 313
Cdd:cd09279  80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 187-311 1.46e-33

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 126.63  E-value: 1.46e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999  187 IIEFDGASKGNPGLSGAAAVLKTEDGSLIFKMR-QGLGIATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMKG 265
Cdd:PRK07238   4 VVEADGGSRGNPGPAGYGAVVWDADRGEVLAERaEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSG 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 30695999  266 QWKVNHEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMA 311
Cdd:PRK07238  84 RWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA 129
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
187-312 4.33e-29

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 108.39  E-value: 4.33e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999 187 IIEFDGASKGNPGLSGAAAVLKteDGSLIFKMRQGLGIATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMKG- 265
Cdd:COG0328   4 EIYTDGACRGNPGPGGWGAVIR--YGGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGw 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30695999 266 --QWKVNH--EVLSK-LHKEAKQLSDKClSFEISHVLRS----LNSDADEQANMAA 312
Cdd:COG0328  82 ihGWKKNGwkPVKNPdLWQRLDELLARH-KVTFEWVKGHaghpGNERADALANKAL 136
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 188-309 3.46e-25

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: 97.77  E-value: 3.46e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999 188 IEFDGASKGNPGLSGAAAVLKTEDGSLIFKMRQGLGIATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMKGQW 267
Cdd:cd06222   1 INVDGSCRGNPGPAGIGGVLRDHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSGS 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 30695999 268 KVNHEVLsKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQAN 309
Cdd:cd06222  81 FKWSPNI-LLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RNAseHI_Thmprot NF041175
ribonuclease HI;
186-314 1.65e-22

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 91.18  E-value: 1.65e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999  186 CIIEFDGASK-GNPGlsGAAA---VLKTEDGSLIfkmrQGLGIA--------TNNAAEYHGLILGLKHAIEKGYTKIKVK 253
Cdd:NF041175   2 AIGYFDGLCEpKNPG--GIATygyVIYLDNKRKI----EGYGLAaepwskdsTNNVAEYTGLICLLEKLLELGISEVIIR 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30695999  254 TDSKLVCMQMKGQWKVNHEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMAARL 314
Cdd:NF041175  76 GDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRIAYEL 136
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 190-311 1.91e-21

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 87.71  E-value: 1.91e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999   190 FDGASKGNPGLSGAAAVLKTEDGSLIFKM-RQGLGIATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMKGQWK 268
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVLLAGqKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSP 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 30695999   269 vNHEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMA 311
Cdd:pfam13456  82 -KQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
rnhA PRK13907
ribonuclease H; Provisional
 188-311 8.98e-17

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 75.47  E-value: 8.98e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999  188 IEFDGASKGNPGLSGAAAVLKTEDGSLifKMRQGLGIATNNAAEYHGLILGLKHAIEKGYTKIKVKTDSKLVCMQMKGQW 267
Cdd:PRK13907   4 VYIDGASKGNPGPSGAGVFIKGVQPAV--QLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 30695999  268 KVNhEVLSKLHKEAKQLSDKCLSFEISHVLRSLNSDADEQANMA 311
Cdd:PRK13907  82 AKN-KMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKA 124
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 191-313 1.22e-10

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: 58.54  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999   191 DGASKGNPGLSGAAAVLKTEDGSLIFkmrQGLGIATNNAAEYHGLILGLKHAIEkgYTKIKVKTDSKLVCM---QMKGQW 267
Cdd:pfam00075   9 DGSCLGNPGPGGAGAVLYRGHENISA---PLPGRTTNNRAELQAVIEALKALKS--PSKVNIYTDSQYVIGgitQWVHGW 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 30695999   268 KVNH--------EVLSK-LHKEAKQLSDKcLSFEISHVlRSLNSDAD-EQANMAAR 313
Cdd:pfam00075  84 KKNGwpttsegkPVKNKdLWQLLKALCKK-HQVYWQWV-KGHAGNPGnEMADRLAK 137
PRK07708 PRK07708
hypothetical protein; Validated
 142-311 1.36e-08

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 54.27  E-value: 1.36e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999  142 ALDLKEDM--FGALTPCLFQDQLpSASMSVEKLAELEPSADTSYETCIIEFDGASKGNPGLSGAAAVLKTEDGSLIFKMR 219
Cdd:PRK07708  29 ALQLAEDFekTGRVKELEFYDEM-DTEWSLKELKKLSKEVEEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIR 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999  220 ---QGLGIATNNAAEYHGLILGLKHAIEKG--YTKIKVKTDSKLVCMQMKGQWKVNHEV----LSKLHKEAKQLSDKCLS 290
Cdd:PRK07708 108 rnaYIEGIYDNNEAEYAALYYAMQELEELGvkHEPVTFRGDSQVVLNQLAGEWPCYDEHlnhwLDRIEQKLKQLKLTPVY 187

                        170       180
                 ....*....|....*....|.
gi 30695999  291 FEIShvlRSLNSDADEQANMA 311
Cdd:PRK07708 188 EPIS---RKQNKEADQLATQA 205
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 191-313 1.97e-08

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: 52.57  E-value: 1.97e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999 191 DGASKGNpGLSGAAAvlktedgslifkmrqGLGI------------------ATNNAAEYHGLILGLKHAIEKGYTKIKV 252
Cdd:cd09280   5 DGSCLNN-GKPGARA---------------GIGVyfgpgdprnvseplpgrkQTNNRAELLAVIHALEQAPEEGIRKLEI 68

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999 253 KTDSKLV--CM------QMKGQWKV-------NHEVLSKLHKEAKQLSDKclsFEISHVlRS-----LNSDADEQANMAA 312
Cdd:cd09280  69 RTDSKYAinCItkwipkWKKNGWKTskgkpvkNQDLIKELDKLLRKRGIK---VKFEHV-KGhsgdpGNEEADRLAREGA 144


                .
gi 30695999 313 R 313
Cdd:cd09280 145 D 145
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 191-270 1.07e-07

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: 50.17  E-value: 1.07e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30695999 191 DGASKGNPGLSGAAAVLktEDGSLIFKMRQGLGIATNNAAEYHGLILGLKhAIEKGYtKIKVKTDSKLV--CMQ--MKGq 266
Cdd:cd09278   7 DGACLGNPGPGGWAAVI--RYGDHEKELSGGEPGTTNNRMELTAAIEALE-ALKEPC-PVTIYTDSQYVinGITkwIKG- 81


                ....
gi 30695999 267 WKVN 270
Cdd:cd09278  82 WKKN 85
 
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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