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Conserved domains on  [gi|530402646|ref|XP_005266582|]
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PREDICTED: ribonuclease H2 subunit B isoform X2 [Homo sapiens]

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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 1.10e-32

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  Cd Length: 211  Bit Score: 120.49  E-value: 1.10e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646  17 VFLVSEYLKDASKkmkngLMFVKLVNPCSGEGAIYLFNMClQQLFEVKVFKE--KHHSWFI-NQSVQSGGLLHFATPVDP 93
Cdd:cd09270    1 VFILPKEATDESQ-----LRIVTLPHPRTGKPTRYLFCPD-GQLYELTAFKEskAPRSWFIgNGTVLQDGSLYVATPFDP 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646  94 LFLLLHYLIKADKE--GKFQPLDQVVVDNVFPNCILL--LKLPGLEKLLHHVTEEKgnpEIDNKKYYKYSKEKTLKWLEK 169
Cdd:cd09270   75 LFLLLPILYKADNKfaGKFLTLDDILDDLSSPSSHLLedLPLPILESSLAKICDVK---EEGDDKFYKYSDEKLLAWLLK 151
                        170
                 ....*....|....*...
gi 530402646 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 1.10e-32

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  Cd Length: 211  Bit Score: 120.49  E-value: 1.10e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646  17 VFLVSEYLKDASKkmkngLMFVKLVNPCSGEGAIYLFNMClQQLFEVKVFKE--KHHSWFI-NQSVQSGGLLHFATPVDP 93
Cdd:cd09270    1 VFILPKEATDESQ-----LRIVTLPHPRTGKPTRYLFCPD-GQLYELTAFKEskAPRSWFIgNGTVLQDGSLYVATPFDP 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646  94 LFLLLHYLIKADKE--GKFQPLDQVVVDNVFPNCILL--LKLPGLEKLLHHVTEEKgnpEIDNKKYYKYSKEKTLKWLEK 169
Cdd:cd09270   75 LFLLLPILYKADNKfaGKFLTLDDILDDLSSPSSHLLedLPLPILESSLAKICDVK---EEGDDKFYKYSDEKLLAWLLK 151
                        170
                 ....*....|....*...
gi 530402646 170 KVNQtvaaLKTNNVNVSS 187
Cdd:cd09270  152 KVER----LKKKELDIKE 165
RNase_H2-Ydr279 pfam09468
Ydr279p protein family (RNase H2 complex component); RNases H are enzymes that specifically ...
14-284 1.47e-61

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


Pssm-ID: 255379  Cd Length: 289  Bit Score: 198.73  E-value: 1.47e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646   14 RQHVFLVSEYLKDAskkmknGLMFVKLVNPCSGEGAIYLFNMCLQQLFEVKVFKE---KHHSWFINQSVQSGGLLHFATP 90
Cdd:pfam09468   1 PSKVFILPKSASNE------NYRIVTLPHPRTGKPARYLFCPKNGQLYELTKIKEskkNPRSWFIGGYVIQNGSLYVATP 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646   91 VDPLFLLLHYLIKADK---EGKFQPLDQVVvDNVFPNCILLLK----LPGLEKLLHHVTEEKgnpEIDNKKYYKYSKEKT 163
Cdd:pfam09468  75 IDPLFLLIPILYKNCTtksKNKFLTLDDIL-DSLYSHLSRLLNweipRPLLEKRLKAVCDVK---EEGDEKFYKLSEEKL 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646  164 LKWLEKKVNQTVAALKTNNVNVSSRVQSTAFFSGDQASTDKEEDYIRYAHGLISDYIPKELSDDLSKYLKLPEPSASLPN 243
Cdd:pfam09468 151 LKWLKAKVERLVKYLPKSKEVSLVRGALSTPLLSSIPEDILELDRLRYACDLLCSYLPKDLYKKLLKSLYDFAPLDKYLK 230
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 530402646  244 PPSKKIKLSDEPVEAKEDYTKFNTKDLKTEKMAAQRQKRGK 284
Cdd:pfam09468 231 ESKKKKRETEEDVEAAESRAEKKRDSKEEIKKKKPKESKGV 271
 
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 1.10e-32

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  Cd Length: 211  Bit Score: 120.49  E-value: 1.10e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646  17 VFLVSEYLKDASKkmkngLMFVKLVNPCSGEGAIYLFNMClQQLFEVKVFKE--KHHSWFI-NQSVQSGGLLHFATPVDP 93
Cdd:cd09270    1 VFILPKEATDESQ-----LRIVTLPHPRTGKPTRYLFCPD-GQLYELTAFKEskAPRSWFIgNGTVLQDGSLYVATPFDP 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646  94 LFLLLHYLIKADKE--GKFQPLDQVVVDNVFPNCILL--LKLPGLEKLLHHVTEEKgnpEIDNKKYYKYSKEKTLKWLEK 169
Cdd:cd09270   75 LFLLLPILYKADNKfaGKFLTLDDILDDLSSPSSHLLedLPLPILESSLAKICDVK---EEGDDKFYKYSDEKLLAWLLK 151
                        170
                 ....*....|....*...
gi 530402646 170 KVNQtvaaLKTNNVNVSS 187
Cdd:cd09270  152 KVER----LKKKELDIKE 165
RNase_H2-Ydr279 pfam09468
Ydr279p protein family (RNase H2 complex component); RNases H are enzymes that specifically ...
14-284 1.47e-61

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


Pssm-ID: 255379  Cd Length: 289  Bit Score: 198.73  E-value: 1.47e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646   14 RQHVFLVSEYLKDAskkmknGLMFVKLVNPCSGEGAIYLFNMCLQQLFEVKVFKE---KHHSWFINQSVQSGGLLHFATP 90
Cdd:pfam09468   1 PSKVFILPKSASNE------NYRIVTLPHPRTGKPARYLFCPKNGQLYELTKIKEskkNPRSWFIGGYVIQNGSLYVATP 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646   91 VDPLFLLLHYLIKADK---EGKFQPLDQVVvDNVFPNCILLLK----LPGLEKLLHHVTEEKgnpEIDNKKYYKYSKEKT 163
Cdd:pfam09468  75 IDPLFLLIPILYKNCTtksKNKFLTLDDIL-DSLYSHLSRLLNweipRPLLEKRLKAVCDVK---EEGDEKFYKLSEEKL 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530402646  164 LKWLEKKVNQTVAALKTNNVNVSSRVQSTAFFSGDQASTDKEEDYIRYAHGLISDYIPKELSDDLSKYLKLPEPSASLPN 243
Cdd:pfam09468 151 LKWLKAKVERLVKYLPKSKEVSLVRGALSTPLLSSIPEDILELDRLRYACDLLCSYLPKDLYKKLLKSLYDFAPLDKYLK 230
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 530402646  244 PPSKKIKLSDEPVEAKEDYTKFNTKDLKTEKMAAQRQKRGK 284
Cdd:pfam09468 231 ESKKKKRETEEDVEAAESRAEKKRDSKEEIKKKKPKESKGV 271
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.12
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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