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Conserved domains on  [gi|767978063|ref|XP_011533533|]
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ribonuclease H2 subunit B isoform X5 [Homo sapiens]

Protein Classification

ribonuclease H2 subunit B( domain architecture ID 10174183)

ribonuclease H2 subunit B is a non-catalytic subunit of RNase H2, 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_H2-B cd09270
Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids; ...
17-187 1.39e-34

Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids; Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. 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. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder.


:

Pssm-ID: 187751 [Multi-domain]  Cd Length: 211  Bit Score: 123.57  E-value: 1.39e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767978063  17 VFLVSEYLKDASKkmkngLMFVKLVNPCSGEGAIYLFNMClQQLFEVKVFKE--KHHSWFI-NQSVQSGGLLHFATPVDP 93
Cdd:cd09270    1 VFILPKEATDESQ-----LRIVTLPHPRTGKPTRYLFCPD-GQLYELTAFKEskAPRSWFIgNGTVLQDGSLYVATPFDP 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767978063  94 LFLLLHYLIKADKE--GKFQPLDQVVVDNVFPNCILL--LKLPGLEKLLHHVTEEKgnpEIDNKKYYKYSKEKTLKWLEK 169
Cdd:cd09270   75 LFLLLPILYKADNKfaGKFLTLDDILDDLSSPSSHLLedLPLPILESSLAKICDVK---EEGDDKFYKYSDEKLLAWLLK 151
                        170
                 ....*....|....*...
gi 767978063 170 KVNQtvaaLKTNNVNVSS 187
Cdd:cd09270  152 KVER----LKKKELDIKE 165
 
Name Accession Description Interval E-value
RNase_H2-B cd09270
Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids; ...
17-187 1.39e-34

Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids; Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. 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. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder.


Pssm-ID: 187751 [Multi-domain]  Cd Length: 211  Bit Score: 123.57  E-value: 1.39e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767978063  17 VFLVSEYLKDASKkmkngLMFVKLVNPCSGEGAIYLFNMClQQLFEVKVFKE--KHHSWFI-NQSVQSGGLLHFATPVDP 93
Cdd:cd09270    1 VFILPKEATDESQ-----LRIVTLPHPRTGKPTRYLFCPD-GQLYELTAFKEskAPRSWFIgNGTVLQDGSLYVATPFDP 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767978063  94 LFLLLHYLIKADKE--GKFQPLDQVVVDNVFPNCILL--LKLPGLEKLLHHVTEEKgnpEIDNKKYYKYSKEKTLKWLEK 169
Cdd:cd09270   75 LFLLLPILYKADNKfaGKFLTLDDILDDLSSPSSHLLedLPLPILESSLAKICDVK---EEGDDKFYKYSDEKLLAWLLK 151
                        170
                 ....*....|....*...
gi 767978063 170 KVNQtvaaLKTNNVNVSS 187
Cdd:cd09270  152 KVER----LKKKELDIKE 165
Ydr279_N pfam17745
Ydr279p protein triple barrel domain; RNases H are enzymes that specifically hydrolyse RNA ...
37-92 6.17e-13

Ydr279p protein triple barrel domain; RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organizms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologs of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. This domain corresponds to the N-terminal triple barrel domain.


Pssm-ID: 465480  Cd Length: 66  Bit Score: 62.24  E-value: 6.17e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767978063   37 FVKLVNPCSGEGAIYLFNMCLQQLFEVKVF---KEKHHSWFI-------NQSVQSGGLLHFATPVD 92
Cdd:pfam17745   1 IVTLPHPRTGSPSRYLLCPETGQLYEFTKIaapKETPRSWLIenendrsDGYVLKDGELLVATPID 66
 
Name Accession Description Interval E-value
RNase_H2-B cd09270
Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids; ...
17-187 1.39e-34

Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids; Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. 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. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder.


Pssm-ID: 187751 [Multi-domain]  Cd Length: 211  Bit Score: 123.57  E-value: 1.39e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767978063  17 VFLVSEYLKDASKkmkngLMFVKLVNPCSGEGAIYLFNMClQQLFEVKVFKE--KHHSWFI-NQSVQSGGLLHFATPVDP 93
Cdd:cd09270    1 VFILPKEATDESQ-----LRIVTLPHPRTGKPTRYLFCPD-GQLYELTAFKEskAPRSWFIgNGTVLQDGSLYVATPFDP 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767978063  94 LFLLLHYLIKADKE--GKFQPLDQVVVDNVFPNCILL--LKLPGLEKLLHHVTEEKgnpEIDNKKYYKYSKEKTLKWLEK 169
Cdd:cd09270   75 LFLLLPILYKADNKfaGKFLTLDDILDDLSSPSSHLLedLPLPILESSLAKICDVK---EEGDDKFYKYSDEKLLAWLLK 151
                        170
                 ....*....|....*...
gi 767978063 170 KVNQtvaaLKTNNVNVSS 187
Cdd:cd09270  152 KVER----LKKKELDIKE 165
Ydr279_N pfam17745
Ydr279p protein triple barrel domain; RNases H are enzymes that specifically hydrolyse RNA ...
37-92 6.17e-13

Ydr279p protein triple barrel domain; RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organizms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologs of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. This domain corresponds to the N-terminal triple barrel domain.


Pssm-ID: 465480  Cd Length: 66  Bit Score: 62.24  E-value: 6.17e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767978063   37 FVKLVNPCSGEGAIYLFNMCLQQLFEVKVF---KEKHHSWFI-------NQSVQSGGLLHFATPVD 92
Cdd:pfam17745   1 IVTLPHPRTGSPSRYLLCPETGQLYEFTKIaapKETPRSWLIenendrsDGYVLKDGELLVATPID 66
RNase_H2-Ydr279 pfam09468
Ydr279p protein family (RNase H2 complex component) wHTH domain; RNases H are enzymes that ...
95-228 1.34e-09

Ydr279p protein family (RNase H2 complex component) wHTH domain; RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organizms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologs of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function.


Pssm-ID: 401427  Cd Length: 157  Bit Score: 55.47  E-value: 1.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767978063   95 FLLLHYLIKADKEGK-----FQPLDQVV--VDNVFPNCILLLKLPGLEKL----LHHVTEEKgnpEIDNKKYYKYSKEKT 163
Cdd:pfam09468   1 FLLLPILYKLTSVSSsekrrFLSLDDILdsLPDSSSHLSELLRSDIPRSLlesrLEAICDTV---EEGDEKMYRLSEEKL 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767978063  164 LKWLEKKVNQTV-----AALKTNNVNVSSRVQSTAFFSGDQASTDKEED--------YIRYAHGLI-SDYIPKELSDDL 228
Cdd:pfam09468  78 LEWLLSKAERMAknllpASLEEKFVKKALEAPLLSVKREEDASTAPIDApeeilqllRLRTALDLIcSSYLPPSLYEKL 156
 
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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