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Conserved domains on  [gi|488224639|ref|WP_002295847|]
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MULTISPECIES: ribonuclease HI family protein [Enterococcus]

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 ...
 2-128 4.91e-43

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: 137.99  E-value: 4.91e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   2 LKVYIDASTKGNPGPSGGGILIVY-QGKQEQLSIPL-SIGTNHQAEFEVFLKTLEFLKKndLQNETIFCFSDSKTLVSTV 79
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSpGGEVLELSERLgFPATNNEAEYEALIAGLELALE--LGAEKLEIYGDSQLVVNQL 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 488224639  80 DKN-ATKNELFLPYLQRIQELLSEFSLLILQWLPENKNKGADNLARQALH 128
Cdd:cd09279   79 NGEyKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 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 ...
 2-128 4.91e-43

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: 137.99  E-value: 4.91e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   2 LKVYIDASTKGNPGPSGGGILIVY-QGKQEQLSIPL-SIGTNHQAEFEVFLKTLEFLKKndLQNETIFCFSDSKTLVSTV 79
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSpGGEVLELSERLgFPATNNEAEYEALIAGLELALE--LGAEKLEIYGDSQLVVNQL 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 488224639  80 DKN-ATKNELFLPYLQRIQELLSEFSLLILQWLPENKNKGADNLARQALH 128
Cdd:cd09279   79 NGEyKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
rnhA PRK13907
ribonuclease H; Provisional
 1-127 2.78e-31

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 108.21  E-value: 2.78e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   1 MLKVYIDASTKGNPGPSGGGILIvyQGKQE--QLSIPLSIGTNHQAEFEVFLKTLEFLKKNdlqNETIFCF-SDSKTLVS 77
Cdd:PRK13907   1 MIEVYIDGASKGNPGPSGAGVFI--KGVQPavQLSLPLGTMSNHEAEYHALLAALKYCTEH---NYNIVSFrTDSQLVER 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 488224639  78 TVDKNATKNELFLPYLQRIQELLSEFSLLILQWLPENKNKGADNLARQAL 127
Cdd:PRK13907  76 AVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAI 125
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1-127 4.19e-27

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 97.61  E-value: 4.19e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   1 MLKVYIDASTKGNPGPSGGGILIVYQGKQEQLSIPLSIGTNHQAEFEVFLKTLEFLKKndLQNETIFCFSDSKTLVSTVD 80
Cdd:COG0328    2 MIEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKE--LGPCEVEIYTDSQYVVNQIT 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488224639  81 K----------NATKNElflPYLQRIQELLSEFSlLILQWLPENK----NKGADNLARQAL 127
Cdd:COG0328   80 GwihgwkkngwKPVKNP---DLWQRLDELLARHK-VTFEWVKGHAghpgNERADALANKAL 136
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 4-127 1.41e-07

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: 47.37  E-value: 1.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639    4 VYIDASTKGNPGPSGGGIlIVYQGKqEQLSIPLSIG-TNHQAEFEVFLKTLEFLKKndlqNETIFCFSDSKTLVSTV--- 79
Cdd:pfam00075   6 VYTDGSCLGNPGPGGAGA-VLYRGH-ENISAPLPGRtTNNRAELQAVIEALKALKS----PSKVNIYTDSQYVIGGItqw 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488224639   80 ----DKNA--TKNElFLPYLQR-IQELLSEFSL---LILQWLPENK----NKGADNLARQAL 127
Cdd:pfam00075  80 vhgwKKNGwpTTSE-GKPVKNKdLWQLLKALCKkhqVYWQWVKGHAgnpgNEMADRLAKQGA 140
 
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 ...
 2-128 4.91e-43

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: 137.99  E-value: 4.91e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   2 LKVYIDASTKGNPGPSGGGILIVY-QGKQEQLSIPL-SIGTNHQAEFEVFLKTLEFLKKndLQNETIFCFSDSKTLVSTV 79
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSpGGEVLELSERLgFPATNNEAEYEALIAGLELALE--LGAEKLEIYGDSQLVVNQL 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 488224639  80 DKN-ATKNELFLPYLQRIQELLSEFSLLILQWLPENKNKGADNLARQALH 128
Cdd:cd09279   79 NGEyKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
rnhA PRK13907
ribonuclease H; Provisional
 1-127 2.78e-31

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 108.21  E-value: 2.78e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   1 MLKVYIDASTKGNPGPSGGGILIvyQGKQE--QLSIPLSIGTNHQAEFEVFLKTLEFLKKNdlqNETIFCF-SDSKTLVS 77
Cdd:PRK13907   1 MIEVYIDGASKGNPGPSGAGVFI--KGVQPavQLSLPLGTMSNHEAEYHALLAALKYCTEH---NYNIVSFrTDSQLVER 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 488224639  78 TVDKNATKNELFLPYLQRIQELLSEFSLLILQWLPENKNKGADNLARQAL 127
Cdd:PRK13907  76 AVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAI 125
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1-127 4.19e-27

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 97.61  E-value: 4.19e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   1 MLKVYIDASTKGNPGPSGGGILIVYQGKQEQLSIPLSIGTNHQAEFEVFLKTLEFLKKndLQNETIFCFSDSKTLVSTVD 80
Cdd:COG0328    2 MIEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKE--LGPCEVEIYTDSQYVVNQIT 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488224639  81 K----------NATKNElflPYLQRIQELLSEFSlLILQWLPENK----NKGADNLARQAL 127
Cdd:COG0328   80 GwihgwkkngwKPVKNP---DLWQRLDELLARHK-VTFEWVKGHAghpgNERADALANKAL 136
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 4-124 1.47e-15

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: 67.72  E-value: 1.47e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   4 VYIDASTKGNPGPSGGGILIV--YQGKQEQLSIPLSIGTNHQAEFEVFLKTLEFLKknDLQNETIFCFSDSKTLVSTVDK 81
Cdd:cd06222    1 INVDGSCRGNPGPAGIGGVLRdhEGGWLGGFALKIGAPTALEAELLALLLALELAL--DLGYLKVIIESDSKYVVDLINS 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 488224639  82 NATKNELFLPYLQRIQELLSEFSLLILQWLPENKNKGADNLAR 124
Cdd:cd06222   79 GSFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1-126 3.48e-08

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: 49.02  E-value: 3.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   1 MLKVYIDASTKGNPGPSGGGILIVYQGKQEQLS--IPLSigTNHQAEFEVFLKTLEFLKkndlQNETIFCFSDSKTLV-- 76
Cdd:cd09278    1 EIVIYTDGACLGNPGPGGWAAVIRYGDHEKELSggEPGT--TNNRMELTAAIEALEALK----EPCPVTIYTDSQYVIng 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488224639  77 -------------STVDKNATKN-ELflpyLQRIQELLsEFSLLILQWLpenknKG---------ADNLARQA 126
Cdd:cd09278   75 itkwikgwkkngwKTADGKPVKNrDL----WQELDALL-AGHKVTWEWV-----KGhaghpgnerADRLANKA 137
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 4-127 1.41e-07

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: 47.37  E-value: 1.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639    4 VYIDASTKGNPGPSGGGIlIVYQGKqEQLSIPLSIG-TNHQAEFEVFLKTLEFLKKndlqNETIFCFSDSKTLVSTV--- 79
Cdd:pfam00075   6 VYTDGSCLGNPGPGGAGA-VLYRGH-ENISAPLPGRtTNNRAELQAVIEALKALKS----PSKVNIYTDSQYVIGGItqw 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488224639   80 ----DKNA--TKNElFLPYLQR-IQELLSEFSL---LILQWLPENK----NKGADNLARQAL 127
Cdd:pfam00075  80 vhgwKKNGwpTTSE-GKPVKNKdLWQLLKALCKkhqVYWQWVKGHAgnpgNEMADRLAKQGA 140
rnhA PRK00203
ribonuclease H; Reviewed
 1-136 8.43e-06

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 42.51  E-value: 8.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   1 MLKVYI--DASTKGNPGPSGGGILIVYQGKQEQLSIPLSIGTNHQAEFEVFLKTLEFLKKN---DLqnetifcFSDSKTL 75
Cdd:PRK00203   1 MKQVEIytDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPcevTL-------YTDSQYV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639  76 V---------------STVDKNATKN-ELFlpylQRIQELLSEFSlLILQWL------PENKNkgADNLARQALHKQLKE 133
Cdd:PRK00203  74 RqgitewihgwkkngwKTADKKPVKNvDLW----QRLDAALKRHQ-IKWHWVkghaghPENER--CDELARAGAEEATLE 146


                 ...
gi 488224639 134 KKT 136
Cdd:PRK00203 147 DTG 149
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 4-126 1.22e-05

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: 41.82  E-value: 1.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   4 VYIDAStkGNPGPSGGGILIVYQGKQEQLSIPLSIGTN-HQAEFEVFLKTLEFLKKNDLQNETIFCFSDSKTLVSTV--D 80
Cdd:cd09276    2 IYTDGS--KLEGSVGAGFVIYRGGEVISRSYRLGTHASvFDAELEAILEALELALATARRARKVTIFTDSQSALQALrnP 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 488224639  81 KNATKNELFLPYLQRIQELLSEFSLLILQWLPENK----NKGADNLARQA 126
Cdd:cd09276   80 RRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVgiegNEAADRLAKEA 129
RNase_H_bacteria_like cd13935
RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence ...
 6-88 1.33e-05

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: 41.74  E-value: 1.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   6 IDASTKGNPGPsgggilIVYQG-----KQEQLSI-PLSIGTNHQAEFEVFLKTLEFLKKndlQNETIFCFSDSKTLVSTV 79
Cdd:cd13935    7 VDAACSGNPGI------VEYRGvdtktGEVLFHRgPFPGGTNNMGEFLAIVHALRYLKE---KNSRKPIYSDSQTAIAWV 77


                 ....*....
gi 488224639  80 DKNATKNEL 88
Cdd:cd13935   78 KKKKAKSTL 86
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 7-127 3.00e-05

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 42.27  E-value: 3.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   7 DASTKGNPGPSGGGILIVYQGKQEQLS-IPLSIG--TNHQAEFEVFLKTLEFLKKndLQNETIFCFSDSKTLV---STVD 80
Cdd:PRK07238   8 DGGSRGNPGPAGYGAVVWDADRGEVLAeRAEAIGraTNNVAEYRGLIAGLEAAAE--LGATEVEVRMDSKLVVeqmSGRW 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 488224639  81 KnaTKNELFLPYLQRIQELLSEFSLLILQWLPENKNKGADNLARQAL 127
Cdd:PRK07238  86 K--VKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAM 130
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 3-126 3.65e-04

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: 37.93  E-value: 3.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   3 KVYIDASTKGN--PGPSGG-GiliVYQGKQEQL--SIPLS--IGTNHQAEFEVFLKTLEFLKKNDLQNETIFcfSDSKTL 75
Cdd:cd09280    1 VVYTDGSCLNNgkPGARAGiG---VYFGPGDPRnvSEPLPgrKQTNNRAELLAVIHALEQAPEEGIRKLEIR--TDSKYA 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488224639  76 VSTVDKNA------------TKNELFLPYLQRIQELLSEFSLLI-LQWLPENK----NKGADNLARQA 126
Cdd:cd09280   76 INCITKWIpkwkkngwktskGKPVKNQDLIKELDKLLRKRGIKVkFEHVKGHSgdpgNEEADRLAREG 143
PRK07708 PRK07708
hypothetical protein; Validated
 4-136 3.69e-04

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 38.86  E-value: 3.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488224639   4 VYIDASTKGNPGPSGGGILIVY-QG-------KQEQLSiplSIGTNHQAEFEVFLKTLEFLKKNDLQNETIFCFSDSKTL 75
Cdd:PRK07708  76 VYFDGGFDKETKLAGLGIVIYYkQGnkryrirRNAYIE---GIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVV 152

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488224639  76 VSTVDKN-ATKNELFLPYLQRIQELLSEFSL-LILQWLPENKNKGADNLARQALHKQLKEKKT 136
Cdd:PRK07708 153 LNQLAGEwPCYDEHLNHWLDRIEQKLKQLKLtPVYEPISRKQNKEADQLATQALEGTVIESHK 215
 
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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