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Conserved domains on  [gi|1958783706|ref|XP_038968439|]
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exonuclease 3'-5' domain-containing protein 2 isoform X1 [Rattus norvegicus]

Protein Classification

3'-5' exonuclease( domain architecture ID 10150121)

3'-5' exonuclease catalyzes the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction; similar to human exonuclease 3'-5' domain-containing protein 2 that that has both 3'-5' exoribonuclease and exodeoxyribonuclease activities

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 109-285 2.61e-54

DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.


:

Pssm-ID: 176653 [Multi-domain]  Cd Length: 170  Bit Score: 183.16  E-value: 2.61e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 109 VSQEAEWNQIqpfLKRELEDFPVLGIDCEWV--NLEGKASPLSLLQMASPSgFCALVRLPRLiyggKTLPRTLLDILADG 186
Cdd:cd06141     1 TDSAQDAEEA---VKELLGKEKVVGFDTEWRpsFRKGKRNKVALLQLATES-RCLLFQLAHM----DKLPPSLKQLLEDP 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 187 TILKVGVGCSEDANKLLQDYGLIVRGCLDLRYLAMKQGNSvlCNGLSLKSLAETLLNFPLDKSLLLRCSNWDAENLTEDQ 266
Cdd:cd06141    73 SILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPR--RKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQ 150

                         170
                  ....*....|....*....
gi 1958783706 267 VTYAARDAQISVALFLHLL 285
Cdd:cd06141   151 ILYAATDAYASLELYRKLL 169
 
Name Accession Description Interval E-value
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 109-285 2.61e-54

DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.


Pssm-ID: 176653 [Multi-domain]  Cd Length: 170  Bit Score: 183.16  E-value: 2.61e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 109 VSQEAEWNQIqpfLKRELEDFPVLGIDCEWV--NLEGKASPLSLLQMASPSgFCALVRLPRLiyggKTLPRTLLDILADG 186
Cdd:cd06141     1 TDSAQDAEEA---VKELLGKEKVVGFDTEWRpsFRKGKRNKVALLQLATES-RCLLFQLAHM----DKLPPSLKQLLEDP 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 187 TILKVGVGCSEDANKLLQDYGLIVRGCLDLRYLAMKQGNSvlCNGLSLKSLAETLLNFPLDKSLLLRCSNWDAENLTEDQ 266
Cdd:cd06141    73 SILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPR--RKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQ 150

                         170
                  ....*....|....*....
gi 1958783706 267 VTYAARDAQISVALFLHLL 285
Cdd:cd06141   151 ILYAATDAYASLELYRKLL 169
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 122-285 6.52e-17

3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.


Pssm-ID: 396266 [Multi-domain]  Cd Length: 173  Bit Score: 78.88  E-value: 6.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 122 LKRELEDFPVLGIDCEWVNL--EGKASPLSLLQMaSPSGFCALvrlPRLIYGGKTLPRTLLDILADGTILKVGVGCSEDA 199
Cdd:pfam01612  13 LIEELLNAPYVAVDTETTSLdtYSYYLRGALIQI-GTGEGAYI---IDPLALGDDVLSALKRLLEDPNITKVGHNAKFDL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 200 NKLLQDYGLIVRGCLDLRYLAMKQGNSVlcnGLSLKSLAETLLNFPLDKSLLlrCSNWDAENLTEDQVTYAARDAQISVA 279
Cdd:pfam01612  89 EVLARDFGIKLRNLFDTMLAAYLLGYDR---SHSLADLAEKYLGVELDKEEQ--CSDWQARPLSEEQLRYAALDADYLLR 163


                  ....*.
gi 1958783706 280 LFLHLL 285
Cdd:pfam01612 164 LYDKLR 169
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 115-285 1.43e-16

3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes


Pssm-ID: 214681 [Multi-domain]  Cd Length: 172  Bit Score: 77.78  E-value: 1.43e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706  115 WNQIQPFLKRELEDFPVLGIDCEWVNLEGKASPLSLLQMASPSGFCALVrlprLIYGGKTLPRTLLDILADGTILKVGVG 194
Cdd:smart00474   7 SETLEELLEKLRAAGGEVALDTETTGLDSYSGKLVLIQISVTGEGAFII----DPLALGDDLEILKDLLEDETITKVGHN 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706  195 CSEDANKLLQdYGLIVRGCLDLRYLAmkqgnSVLCNGLS---LKSLAETLLNFPLDKSLllRCSNWDAENLTEDQVTYAA 271
Cdd:smart00474  83 AKFDLHVLAR-FGIELENIFDTMLAA-----YLLLGGPSkhgLATLLLGYLGVELDKEE--QKSDWGARPLSEEQLEYAA 154

                          170
                   ....*....|....
gi 1958783706  272 RDAQISVALFLHLL 285
Cdd:smart00474 155 EDADALLRLYEKLE 168
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
117-273 1.25e-10

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 63.35  E-value: 1.25e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 117 QIQPFLKReLEDFPVLGIDCEWVNLEGKASPLSLLQMASPSGfCALVRlprlIYGGKTLPRtLLDILADGTILKVGVGCS 196
Cdd:COG0349     7 ELAALCAR-LAQAPAVAVDTEFMRERTYYPRLCLIQLADGEE-VALID----PLAIGDLSP-LWELLADPAIVKVFHAAR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 197 EDANKLLQDYGLIVRGCLDLRYLAMkqgnsvLCN---GLSLKSLAETLLNFPLDKSLllRCSNWDAENLTEDQVTYAARD 273
Cdd:COG0349    80 EDLEILYHLFGILPKPLFDTQIAAA------LLGygdSVGYAALVEELLGVELDKSE--QRSDWLRRPLSEEQLEYAAAD 151
 
Name Accession Description Interval E-value
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 109-285 2.61e-54

DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.


Pssm-ID: 176653 [Multi-domain]  Cd Length: 170  Bit Score: 183.16  E-value: 2.61e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 109 VSQEAEWNQIqpfLKRELEDFPVLGIDCEWV--NLEGKASPLSLLQMASPSgFCALVRLPRLiyggKTLPRTLLDILADG 186
Cdd:cd06141     1 TDSAQDAEEA---VKELLGKEKVVGFDTEWRpsFRKGKRNKVALLQLATES-RCLLFQLAHM----DKLPPSLKQLLEDP 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 187 TILKVGVGCSEDANKLLQDYGLIVRGCLDLRYLAMKQGNSvlCNGLSLKSLAETLLNFPLDKSLLLRCSNWDAENLTEDQ 266
Cdd:cd06141    73 SILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPR--RKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQ 150

                         170
                  ....*....|....*....
gi 1958783706 267 VTYAARDAQISVALFLHLL 285
Cdd:cd06141   151 ILYAATDAYASLELYRKLL 169
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
 128-274 2.87e-19

DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif.


Pssm-ID: 176650 [Multi-domain]  Cd Length: 161  Bit Score: 85.26  E-value: 2.87e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 128 DFPVLGIDCEWVNLEGKASPLSLLQMASPSGFCALVRLPRLiyggKTLPRTLLDILADGTILKVGVGCSEDANKLLQDYG 207
Cdd:cd06129    12 DGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSL----SVDWQGLKMLLENPSIVKALHGIEGDLWKLLRDFG 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958783706 208 LIVRGCLDLRYLAMKQGnsvLCNGLSLKSLAETLLNFPLDKSLllRCSNWDAENLTEDQVTYAARDA 274
Cdd:cd06129    88 EKLQRLFDTTIAANLKG---LPERWSLASLVEHFLGKTLDKSI--SCADWSYRPLTEDQKLYAAADV 149
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
 122-285 2.56e-18

DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.


Pssm-ID: 176655  Cd Length: 193  Bit Score: 83.50  E-value: 2.56e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 122 LKRELEDFPVLGIDCEW--VNLEGKASPLSLLQMASPSG-FcaLVRLPRLIYGG-KTLPRTLLDILADGTILKVGVGCSE 197
Cdd:cd06146    15 LALSLEAGRVVGIDSEWkpSFLGDSDPRVAILQLATEDEvF--LLDLLALENLEsEDWDRLLKRLFEDPDVLKLGFGFKQ 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 198 DANKL------LQDYGLIVRGCLDLRYLA---MKQGNSVLCNGL-----SLKSLAETLLNFPLDKSLllRCSNWDAENLT 263
Cdd:cd06146    93 DLKALsasypaLKCMFERVQNVLDLQNLAkelQKSDMGRLKGNLpsktkGLADLVQEVLGKPLDKSE--QCSNWERRPLR 170

                         170       180
                  ....*....|....*....|..
gi 1958783706 264 EDQVTYAARDAQISVALFLHLL 285
Cdd:cd06146   171 EEQILYAALDAYCLLEVFDKLL 192
DEDDy_polA_RNaseD_like_exo cd09018
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ...
 131-284 1.55e-17

DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity.


Pssm-ID: 176656 [Multi-domain]  Cd Length: 150  Bit Score: 79.98  E-value: 1.55e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 131 VLGIDCEWVNLEGKASPLSLLQMASPSGFCALVRlprlIYGGKTLPRTLLDILADGTILKVGVGCSEDANKLLQDYGLIV 210
Cdd:cd09018     1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIP----VAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELR 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958783706 211 RGCLDLRYLAMKQGNSVLCNGLSlkSLAETLLNFPLDKSLLLRCSNWDAENLTEDQVTYAARDAQISVALFLHL 284
Cdd:cd09018    77 GIAFDTMLEAYILNSVAGRWDMD--SLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKL 148
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 122-285 6.52e-17

3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.


Pssm-ID: 396266 [Multi-domain]  Cd Length: 173  Bit Score: 78.88  E-value: 6.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 122 LKRELEDFPVLGIDCEWVNL--EGKASPLSLLQMaSPSGFCALvrlPRLIYGGKTLPRTLLDILADGTILKVGVGCSEDA 199
Cdd:pfam01612  13 LIEELLNAPYVAVDTETTSLdtYSYYLRGALIQI-GTGEGAYI---IDPLALGDDVLSALKRLLEDPNITKVGHNAKFDL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 200 NKLLQDYGLIVRGCLDLRYLAMKQGNSVlcnGLSLKSLAETLLNFPLDKSLLlrCSNWDAENLTEDQVTYAARDAQISVA 279
Cdd:pfam01612  89 EVLARDFGIKLRNLFDTMLAAYLLGYDR---SHSLADLAEKYLGVELDKEEQ--CSDWQARPLSEEQLRYAALDADYLLR 163


                  ....*.
gi 1958783706 280 LFLHLL 285
Cdd:pfam01612 164 LYDKLR 169
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 115-285 1.43e-16

3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes


Pssm-ID: 214681 [Multi-domain]  Cd Length: 172  Bit Score: 77.78  E-value: 1.43e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706  115 WNQIQPFLKRELEDFPVLGIDCEWVNLEGKASPLSLLQMASPSGFCALVrlprLIYGGKTLPRTLLDILADGTILKVGVG 194
Cdd:smart00474   7 SETLEELLEKLRAAGGEVALDTETTGLDSYSGKLVLIQISVTGEGAFII----DPLALGDDLEILKDLLEDETITKVGHN 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706  195 CSEDANKLLQdYGLIVRGCLDLRYLAmkqgnSVLCNGLS---LKSLAETLLNFPLDKSLllRCSNWDAENLTEDQVTYAA 271
Cdd:smart00474  83 AKFDLHVLAR-FGIELENIFDTMLAA-----YLLLGGPSkhgLATLLLGYLGVELDKEE--QKSDWGARPLSEEQLEYAA 154

                          170
                   ....*....|....
gi 1958783706  272 RDAQISVALFLHLL 285
Cdd:smart00474 155 EDADALLRLYEKLE 168
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 122-273 2.17e-13

DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.


Pssm-ID: 176654 [Multi-domain]  Cd Length: 178  Bit Score: 68.71  E-value: 2.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 122 LKRELEDFPVLGIDCEWVNLEGKASPLSLLQMASPSGfCALVRLPRLiyggKTLPRtLLDILADGTILKVGVGCSEDANK 201
Cdd:cd06142     5 LCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGE-VYLIDPLAI----GDLSP-LKELLADPNIVKVFHAAREDLEL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958783706 202 LLQDYGLIVRGCLDLrYLAMKqgnsvLCN---GLSLKSLAETLLNFPLDKSLllRCSNWDAENLTEDQVTYAARD 273
Cdd:cd06142    79 LKRDFGILPQNLFDT-QIAAR-----LLGlgdSVGLAALVEELLGVELDKGE--QRSDWSKRPLTDEQLEYAALD 145
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
117-273 1.25e-10

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 63.35  E-value: 1.25e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 117 QIQPFLKReLEDFPVLGIDCEWVNLEGKASPLSLLQMASPSGfCALVRlprlIYGGKTLPRtLLDILADGTILKVGVGCS 196
Cdd:COG0349     7 ELAALCAR-LAQAPAVAVDTEFMRERTYYPRLCLIQLADGEE-VALID----PLAIGDLSP-LWELLADPAIVKVFHAAR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 197 EDANKLLQDYGLIVRGCLDLRYLAMkqgnsvLCN---GLSLKSLAETLLNFPLDKSLllRCSNWDAENLTEDQVTYAARD 273
Cdd:COG0349    80 EDLEILYHLFGILPKPLFDTQIAAA------LLGygdSVGYAALVEELLGVELDKSE--QRSDWLRRPLSEEQLEYAAAD 151
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
 179-274 7.19e-04

DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins; Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.


Pssm-ID: 99850 [Multi-domain]  Cd Length: 192  Bit Score: 41.04  E-value: 7.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 179 LLDILADGTILKVGVGCSEDANKLLQDYGLIVRGCLDlRYLAMKqgnsVLC-NGLSLKSLAETLLNFPLDKSLLLrcSNW 257
Cdd:cd06147    69 LNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFD-TGQAAR----VLNlPRHSLAYLLQKYCNVDADKKYQL--ADW 141

                          90
                  ....*....|....*..
gi 1958783706 258 DAENLTEDQVTYAARDA 274
Cdd:cd06147   142 RIRPLPEEMIKYAREDT 158
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 131-285 3.27e-03

DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.


Pssm-ID: 99851  Cd Length: 197  Bit Score: 39.19  E-value: 3.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 131 VLGIDCEWVNLeGKASPLSLLQMASPSG----FCALVRLPRLIYGGktlprtLLDILADGTILKVGVGCSEDANKLLQDY 206
Cdd:cd06148    12 VIGLDCEGVNL-GRKGKLCLVQIATRTGqiylFDILKLGSIVFING------LKDILESKKILKVIHDCRRDSDALYHQY 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783706 207 GLIVRGCLD-------LRYlaMKQGNSVLCNGLSLKSLAETLL----NFPLDKSLLLR--CSNWDAENLTEDQVTYAARD 273
Cdd:cd06148    85 GIKLNNVFDtqvadalLQE--QETGGFNPDRVISLVQLLDKYLyisiSLKEDVKKLMRedPKFWALRPLTEDMIRYAALD 162

                         170
                  ....*....|..
gi 1958783706 274 AQISVALFLHLL 285
Cdd:cd06148   163 VLCLLPLYYAML 174
 
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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