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Conserved domains on  [gi|1958747083|ref|XP_038953836|]
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ribonuclease H2 subunit A isoform X1 [Rattus norvegicus]

Protein Classification

ribonuclease H2 subunit A( domain architecture ID 10163194)

ribonuclease H2 subunit A is the catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HII_eukaryota_like cd07181
Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which ...
 18-158 8.73e-99

Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which is active during replication and is believed to play a role in the removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII (RNASEH2A) is functional when it forms a heterotrimeric complex with two other accessory proteins (RNASEH2B and RNASEH2C). It is speculated that these accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause the severe genetic neurological disorder Aicardi-Goutieres syndrome. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms.


:

Pssm-ID: 260002  Cd Length: 221  Bit Score: 285.57  E-value: 8.73e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  18 KYNLNSMSHDTAAGLIQHAMDQNVKVTQVFVDTVGMPETYQARLQQRFPGIEVTVKAKADSLFPVVSAASIIAKVARDQA 97
Cdd:cd07181    81 KYNLNEISHDAAIGLIRSVLDKGVNVTEVYVDTVGPPEKYQAKLQKLFPGIKITVSKKADSLYPIVSAASIVAKVTRDRA 160

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958747083  98 VKNWQFVESLQGLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAE 158
Cdd:cd07181   161 LENWQFEEPGIDIDREFGSGYPSDPKTKAWLKKNVDPVFGFPSLVRFSWSTAKTILEKKAV 221
 
Name Accession Description Interval E-value
RNase_HII_eukaryota_like cd07181
Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which ...
 18-158 8.73e-99

Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which is active during replication and is believed to play a role in the removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII (RNASEH2A) is functional when it forms a heterotrimeric complex with two other accessory proteins (RNASEH2B and RNASEH2C). It is speculated that these accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause the severe genetic neurological disorder Aicardi-Goutieres syndrome. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms.


Pssm-ID: 260002  Cd Length: 221  Bit Score: 285.57  E-value: 8.73e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  18 KYNLNSMSHDTAAGLIQHAMDQNVKVTQVFVDTVGMPETYQARLQQRFPGIEVTVKAKADSLFPVVSAASIIAKVARDQA 97
Cdd:cd07181    81 KYNLNEISHDAAIGLIRSVLDKGVNVTEVYVDTVGPPEKYQAKLQKLFPGIKITVSKKADSLYPIVSAASIVAKVTRDRA 160

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958747083  98 VKNWQFVESLQGLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAE 158
Cdd:cd07181   161 LENWQFEEPGIDIDREFGSGYPSDPKTKAWLKKNVDPVFGFPSLVRFSWSTAKTILEKKAV 221
TIGR00729 TIGR00729
ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA ...
 19-154 1.87e-36

ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA hybrids. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129812  Cd Length: 206  Bit Score: 126.43  E-value: 1.87e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  19 YNLNSMSHDTAAGLIQHAMDQNVKVtqvFVDTVGMPE---TYQARLQQRFPGIEVTVKAKADSLFPVVSAASIIAKVARD 95
Cdd:TIGR00729  77 INLNENEIEKFSKAAIILIEKPSEV---YVDSVDVNPkrfKREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVERD 153

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958747083  96 QAVknwqfvESLQGLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILE 154
Cdd:TIGR00729 154 REI------ESLKRKYGDFGSGYPSDPRTREWLEEYFKSHGELPDIVRRTWKTVRKLLD 206
RNase_HII pfam01351
Ribonuclease HII;
18-149 4.94e-32

Ribonuclease HII;


Pssm-ID: 396082  Cd Length: 199  Bit Score: 114.79  E-value: 4.94e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  18 KYNLNSMSHDTAAGLIQHAMDQNVKVTQVFVDTVGMPETYQARLQQRFpGIEVTVKAKADSLFPVVSAASIIAKVARDqa 97
Cdd:pfam01351  74 EINLNEIKAALHLAMIRLLEKLGVKPDEILVDGFRPPGSLPKKLRDIF-GIKVTAEHKADGKYLAVAAASIIAKVERD-- 150

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958747083  98 vknwQFVESLQ---GLDSDYGSGYPNDPKTKAWLRKHVDPvfGFPQFVRFSWSTA 149
Cdd:pfam01351 151 ----EMLELLKrfpGYGLDKGSGYGSDPHTRALLKLGGTP--WLPDFHRLSFKTV 199
RnhB COG0164
Ribonuclease HII [Replication, recombination and repair];
64-153 1.27e-16

Ribonuclease HII [Replication, recombination and repair];


Pssm-ID: 439934  Cd Length: 190  Bit Score: 74.33  E-value: 1.27e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  64 RFPGIEVTVKA--KADSLFPVVSAASIIAKVARDQAVknwqfveslQGLDSDY-------GSGYPNDPkTKAWLRKHvdp 134
Cdd:COG0164   107 RLPGLPIPVEAivKGDAKSASIAAASILAKVTRDRLM---------EELDEEYpgygfakHKGYPTKE-HREALREY--- 173

                          90
                  ....*....|....*....
gi 1958747083 135 vfGFPQFVRFSWSTAQAIL 153
Cdd:COG0164   174 --GPTPIHRRSFAPVKKLL 190
rnhB PRK00015
ribonuclease HII; Validated
 64-148 1.71e-16

ribonuclease HII; Validated


Pssm-ID: 234574  Cd Length: 197  Bit Score: 74.04  E-value: 1.71e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  64 RFPGIEVTVKA--KADSLFPVVSAASIIAKVARDQAVKNwqfveslqgLDSDYG-------SGYPNDPKTKAWLRkhvdp 134
Cdd:PRK00015  118 RVPKLPIPQEAivKGDAKSPSIAAASILAKVTRDRLMEE---------LDKEYPgygfakhKGYGTKEHLEALAK----- 183

                          90
                  ....*....|....
gi 1958747083 135 vFGFPQFVRFSWST 148
Cdd:PRK00015  184 -YGPTPIHRRSFAP 196
 
Name Accession Description Interval E-value
RNase_HII_eukaryota_like cd07181
Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which ...
 18-158 8.73e-99

Eukaryotic RNase HII; This family includes eukaryotic type 2 RNase H (RNase HII or H2) which is active during replication and is believed to play a role in the removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII (RNASEH2A) is functional when it forms a heterotrimeric complex with two other accessory proteins (RNASEH2B and RNASEH2C). It is speculated that these accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause the severe genetic neurological disorder Aicardi-Goutieres syndrome. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms.


Pssm-ID: 260002  Cd Length: 221  Bit Score: 285.57  E-value: 8.73e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  18 KYNLNSMSHDTAAGLIQHAMDQNVKVTQVFVDTVGMPETYQARLQQRFPGIEVTVKAKADSLFPVVSAASIIAKVARDQA 97
Cdd:cd07181    81 KYNLNEISHDAAIGLIRSVLDKGVNVTEVYVDTVGPPEKYQAKLQKLFPGIKITVSKKADSLYPIVSAASIVAKVTRDRA 160

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958747083  98 VKNWQFVESLQGLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAE 158
Cdd:cd07181   161 LENWQFEEPGIDIDREFGSGYPSDPKTKAWLKKNVDPVFGFPSLVRFSWSTAKTILEKKAV 221
RNase_HII cd06266
Ribonuclease H (RNase H) type II family (prokaryotic RNase HII and HIII, and eukaryotic RNase ...
 18-148 4.10e-52

Ribonuclease H (RNase H) type II family (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII); This family contains ribonucleases HII (RNases H2) which include bacterial RNase HII and HIII, and eukaryotic and archaeal RNase H2/HII. RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thereby preventing genomic instability and the accumulation of aberrant nucleic acid which can induce Aicardi-Goutieres syndrome, a severe autoimmune disorder in humans. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, but no prokaryotic genome contains the combination of only RNase HI and HIII. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli.


Pssm-ID: 259999  Cd Length: 193  Bit Score: 166.23  E-value: 4.10e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  18 KYNLNSMSHDTAAGLIQHAmdqNVKVTQVFVDTVGMPETYQARLQQRFPGIEVTVKAKADSLFPVVSAASIIAKVARDQA 97
Cdd:cd06266    73 AKNINNATKLAYNRALENL---SVKPEFVLVDGKGIEPEYLSRELEEILGVRVTCLVKADSKSPLVAAASIIAKVFRDRE 149

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958747083  98 VKNWQFVESLQgldsdyGSGYPNDPKTKAWLRKHVDPVFgFPQFVRFSWST 148
Cdd:cd06266   150 MEELHRKYGLF------GSGYYADPETLEELRKNIVLGR-IPPCVRLSFET 193
TIGR00729 TIGR00729
ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA ...
 19-154 1.87e-36

ribonuclease H, mammalian HI/archaeal HII subfamily; This enzyme cleaves RNA from DNA-RNA hybrids. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129812  Cd Length: 206  Bit Score: 126.43  E-value: 1.87e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  19 YNLNSMSHDTAAGLIQHAMDQNVKVtqvFVDTVGMPE---TYQARLQQRFPGIEVTVKAKADSLFPVVSAASIIAKVARD 95
Cdd:TIGR00729  77 INLNENEIEKFSKAAIILIEKPSEV---YVDSVDVNPkrfKREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVERD 153

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958747083  96 QAVknwqfvESLQGLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILE 154
Cdd:TIGR00729 154 REI------ESLKRKYGDFGSGYPSDPRTREWLEEYFKSHGELPDIVRRTWKTVRKLLD 206
RNase_HII_archaea_like cd07180
Archaeal Ribonuclease HII; This family includes type 2 RNases H from archaea, some of which ...
 20-153 1.92e-33

Archaeal Ribonuclease HII; This family includes type 2 RNases H from archaea, some of which show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one is involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair.


Pssm-ID: 260001  Cd Length: 204  Bit Score: 118.81  E-value: 1.92e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  20 NLNSMSHDTAAGLIQHAMDQNVKVtqvFVDTVGM-PETYQARLQQRF-PGIEVTVKAKADSLFPVVSAASIIAKVARDQA 97
Cdd:cd07180    78 NLNELEAEAFAEIINRLALQPDTV---YVDACDVnEERFGRRLRERLnTGVEVVAEHKADAKYPVVSAASIVAKVERDRE 154

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958747083  98 VknwqfvESLQGLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAIL 153
Cdd:cd07180   155 I------EELKKEYGDFGSGYPSDPKTIEFLREYYREHGEPPPIVRKSWKTVKRLL 204
RNase_HII pfam01351
Ribonuclease HII;
18-149 4.94e-32

Ribonuclease HII;


Pssm-ID: 396082  Cd Length: 199  Bit Score: 114.79  E-value: 4.94e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  18 KYNLNSMSHDTAAGLIQHAMDQNVKVTQVFVDTVGMPETYQARLQQRFpGIEVTVKAKADSLFPVVSAASIIAKVARDqa 97
Cdd:pfam01351  74 EINLNEIKAALHLAMIRLLEKLGVKPDEILVDGFRPPGSLPKKLRDIF-GIKVTAEHKADGKYLAVAAASIIAKVERD-- 150

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958747083  98 vknwQFVESLQ---GLDSDYGSGYPNDPKTKAWLRKHVDPvfGFPQFVRFSWSTA 149
Cdd:pfam01351 151 ----EMLELLKrfpGYGLDKGSGYGSDPHTRALLKLGGTP--WLPDFHRLSFKTV 199
RnhB COG0164
Ribonuclease HII [Replication, recombination and repair];
64-153 1.27e-16

Ribonuclease HII [Replication, recombination and repair];


Pssm-ID: 439934  Cd Length: 190  Bit Score: 74.33  E-value: 1.27e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  64 RFPGIEVTVKA--KADSLFPVVSAASIIAKVARDQAVknwqfveslQGLDSDY-------GSGYPNDPkTKAWLRKHvdp 134
Cdd:COG0164   107 RLPGLPIPVEAivKGDAKSASIAAASILAKVTRDRLM---------EELDEEYpgygfakHKGYPTKE-HREALREY--- 173

                          90
                  ....*....|....*....
gi 1958747083 135 vfGFPQFVRFSWSTAQAIL 153
Cdd:COG0164   174 --GPTPIHRRSFAPVKKLL 190
rnhB PRK00015
ribonuclease HII; Validated
 64-148 1.71e-16

ribonuclease HII; Validated


Pssm-ID: 234574  Cd Length: 197  Bit Score: 74.04  E-value: 1.71e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  64 RFPGIEVTVKA--KADSLFPVVSAASIIAKVARDQAVKNwqfveslqgLDSDYG-------SGYPNDPKTKAWLRkhvdp 134
Cdd:PRK00015  118 RVPKLPIPQEAivKGDAKSPSIAAASILAKVTRDRLMEE---------LDKEYPgygfakhKGYGTKEHLEALAK----- 183

                          90
                  ....*....|....
gi 1958747083 135 vFGFPQFVRFSWST 148
Cdd:PRK00015  184 -YGPTPIHRRSFAP 196
RNase_HII_bacteria_HIII_like cd06590
Bacterial type 2 ribonuclease, HII and HIII-like; This family includes type 2 RNases H from ...
 18-119 8.05e-09

Bacterial type 2 ribonuclease, HII and HIII-like; This family includes type 2 RNases H from several bacteria, such as Bacillus subtilis, which have two different RNases, HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic "DEDD" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes; however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gene inheritance might be the result of functional redundancy of RNase HI and HIII in prokaryotes. Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair.


Pssm-ID: 260000  Cd Length: 207  Bit Score: 53.29  E-value: 8.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  18 KYNLNSM---SHDTAaglIQHAMDQNVKVTQVFVDTVGMPETYQARLQQ-RFPGIEVTVKAKADSLFPVVSAASIIAKVA 93
Cdd:cd06590    77 GKNLNKLkawLHNQA---IENLLKKKKKPKFILIDQFASEKVYYNYLKKeKIKKIPLYFETKAESKDLAVAAASILARYA 153

                          90       100
                  ....*....|....*....|....*.
gi 1958747083  94 rdqavknwqFVESLQGLDSDYGSGYP 119
Cdd:cd06590   154 ---------FLEEMDKLSKEYGMKLP 170
RNase_HII_bacteria_HII_like cd07182
Bacterial Ribonuclease HII-like; This family includes mostly bacterial type 2 RNases H, with ...
 64-96 1.97e-07

Bacterial Ribonuclease HII-like; This family includes mostly bacterial type 2 RNases H, with some eukaryotic members. Bacterial RNase HII has a role in primer removal based on its involvement in ribonucleotide-specific catalytic activity in the presence of RNA/DNA hybrid substrates. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII; double deletion of these leads to cellular lethality. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype. In Leishmania mitochondria, of the four distinct RNase H genes (H1, HIIA, HIIB, HIIC), HIIC is essential for the survival of the parasite and thus can be a potential target for anti-leishmanial chemotherapy. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair.


Pssm-ID: 260003  Cd Length: 177  Bit Score: 48.91  E-value: 1.97e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958747083  64 RFPGIEVTVKA--KADSLFPVVSAASIIAKVARDQ 96
Cdd:cd07182    99 RLPPLPIPQEAivKGDAKSASIAAASILAKVTRDR 133
RnhC COG1039
Ribonuclease HIII [Replication, recombination and repair];
19-115 8.52e-07

Ribonuclease HIII [Replication, recombination and repair];


Pssm-ID: 440661 [Multi-domain]  Cd Length: 302  Bit Score: 48.32  E-value: 8.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747083  19 YNLNSM---SHDTAaglIQHAMDQNVKVTQVFVDTVGMPETYQARLQQR--FPGIEVTVKAKADSLFPVVSAASIIAKVA 93
Cdd:COG1039   170 WNLNKLkawLHNQA---IENLLKKIAKPDGILIDQFAEPKVYFKYLKKEknIVRENLYFRTKAESDHLAVAAASIIARAA 246

                          90       100
                  ....*....|....*....|..
gi 1958747083  94 rdqavknwqFVESLQGLDSDYG 115
Cdd:COG1039   247 ---------FLKEMDKLSKEAG 259
rnhB PRK13925
ribonuclease HII; Provisional
 66-99 9.05e-04

ribonuclease HII; Provisional


Pssm-ID: 184399  Cd Length: 198  Bit Score: 38.84  E-value: 9.05e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1958747083  66 PGIEVTVkAKADSLFPVVSAASIIAKVARDQAVK 99
Cdd:PRK13925  119 PGPQRTI-VKGDSKSAAIAAASILAKVWRDDLIK 151
 
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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