NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2024361882|ref|XP_040505102|]
View 

exonuclease mut-7 homolog isoform X4 [Gallus gallus]

Protein Classification

exonuclease mut-7 family protein; 3'-5' exonuclease( domain architecture ID 10150257)

exonuclease mut-7 family protein belonging to the DnaQ-like (or DEDD) 3'-5' exonuclease superfamily may catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction| 3'-5' exonuclease has a fundamental role in reducing polymerase errors and is involved in proofreading activity

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
 385-597 5.19e-80

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: 256.84  E-value: 5.19e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 385 IRLLQNWEEMMQCYEKV-LKPGQIVGIDMEWRPSFGMVGKPRVSLLQLAVRDEVFLLDLPRLLeqaevKGEKEKLPHFIQ 463
Cdd:cd06146     1 IHIVDSEEELEALLLALsLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALE-----NLESEDWDRLLK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 464 RLYSDATITKLGYGMSGDLSSLAATCSTLKGMDKQSQSVVDLLTIDKLLQKSSTDWKKGGLkvdvlspeqscedgglRQP 543
Cdd:cd06146    76 RLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNL----------------PSK 139

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2024361882 544 EKGLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCK 597
Cdd:cd06146   140 TKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193
Mut7-C super family cl19501
Mut7-C RNAse domain; RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C ...
 654-748 5.42e-13

Mut7-C RNAse domain; RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C terminus.


The actual alignment was detected with superfamily member pfam01927:

Pssm-ID: 473177  Cd Length: 146  Bit Score: 67.28  E-value: 5.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 654 VCDNMLQGLGRYLRCLGVDVRMLENEDDhRKAAEIARQEGRVILT--SGLpyqtLRSHVGEGRCFSvnCSEKAKEQALQV 731
Cdd:pfam01927   4 LLDAMLGKLARYLRMLGYDTLYDNDYED-DELLRIAAKEGRILLTrdRGL----LKRRELTHGVYV--RSLDPEEQLREV 76

                          90
                  ....*....|....*..
gi 2024361882 732 LKHFNVHVTLADIFSRC 748
Cdd:pfam01927  77 IARLGLALSLKPEFSRC 93
 
Name Accession Description Interval E-value
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
 385-597 5.19e-80

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: 256.84  E-value: 5.19e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 385 IRLLQNWEEMMQCYEKV-LKPGQIVGIDMEWRPSFGMVGKPRVSLLQLAVRDEVFLLDLPRLLeqaevKGEKEKLPHFIQ 463
Cdd:cd06146     1 IHIVDSEEELEALLLALsLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALE-----NLESEDWDRLLK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 464 RLYSDATITKLGYGMSGDLSSLAATCSTLKGMDKQSQSVVDLLTIDKLLQKSSTDWKKGGLkvdvlspeqscedgglRQP 543
Cdd:cd06146    76 RLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNL----------------PSK 139

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2024361882 544 EKGLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCK 597
Cdd:cd06146   140 TKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 398-595 3.44e-21

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: 91.59  E-value: 3.44e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 398 YEKVLKPGQIVGIDMEWRPSFGMVGKPRVSLLQLAVRDEVFLLDlPRLLEQAEVkgekeklpHFIQRLYSDATITKLGYG 477
Cdd:pfam01612  13 LIEELLNAPYVAVDTETTSLDTYSYYLRGALIQIGTGEGAYIID-PLALGDDVL--------SALKRLLEDPNITKVGHN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 478 MSGDLSSLAatcsTLKGMDKQSqsvvdllTIDKLLQKSstdwkkgglkvdVLSPEQScedgglrqpeKGLSLLVQHVLGK 557
Cdd:pfam01612  84 AKFDLEVLA----RDFGIKLRN-------LFDTMLAAY------------LLGYDRS----------HSLADLAEKYLGV 130

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2024361882 558 PLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKL 595
Cdd:pfam01612 131 ELDKEEQCSDWQARPLSEEQLRYAALDADYLLRLYDKL 168
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 399-595 4.89e-17

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: 79.71  E-value: 4.89e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882  399 EKVLKPGQIVGIDMEWRPsfGMVGKPRVSLLQLAV-RDEVFLLDLPRLLEQAEVkgekeklphfIQRLYSDATITKLGYG 477
Cdd:smart00474  15 EKLRAAGGEVALDTETTG--LDSYSGKLVLIQISVtGEGAFIIDPLALGDDLEI----------LKDLLEDETITKVGHN 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882  478 MSGDLSSLAATCSTLKGMdkqsqsvVDLLTIDKLLQKSSTDWkkgglkvdvlspeqscedgglrqpekGLSLLVQHVLGK 557
Cdd:smart00474  83 AKFDLHVLARFGIELENI-------FDTMLAAYLLLGGPSKH--------------------------GLATLLLGYLGV 129

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 2024361882  558 PLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKL 595
Cdd:smart00474 130 ELDKEEQKSDWGARPLSEEQLEYAAEDADALLRLYEKL 167
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
546-597 5.09e-14

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 74.52  E-value: 5.09e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2024361882 546 GLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCK 597
Cdd:COG0349   113 GYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYEKLLE 164
Mut7-C pfam01927
Mut7-C RNAse domain; RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C ...
 654-748 5.42e-13

Mut7-C RNAse domain; RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C terminus.


Pssm-ID: 426515  Cd Length: 146  Bit Score: 67.28  E-value: 5.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 654 VCDNMLQGLGRYLRCLGVDVRMLENEDDhRKAAEIARQEGRVILT--SGLpyqtLRSHVGEGRCFSvnCSEKAKEQALQV 731
Cdd:pfam01927   4 LLDAMLGKLARYLRMLGYDTLYDNDYED-DELLRIAAKEGRILLTrdRGL----LKRRELTHGVYV--RSLDPEEQLREV 76

                          90
                  ....*....|....*..
gi 2024361882 732 LKHFNVHVTLADIFSRC 748
Cdd:pfam01927  77 IARLGLALSLKPEFSRC 93
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 546-595 5.80e-08

ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. [Transcription, RNA processing]


Pssm-ID: 130455 [Multi-domain]  Cd Length: 367  Bit Score: 55.93  E-value: 5.80e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2024361882 546 GLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKL 595
Cdd:TIGR01388 113 GYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKL 162
PRK10829 PRK10829
ribonuclease D; Provisional
 546-603 1.18e-06

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 51.93  E-value: 1.18e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2024361882 546 GLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCKDPESFG 603
Cdd:PRK10829  117 GFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAG 174
PIN_Mut7-C-like cd18771
uncharacterized subgroup of the Mut7-C-like family of the PIN domain superfamily; The ...
 654-698 8.56e-03

uncharacterized subgroup of the Mut7-C-like family of the PIN domain superfamily; The Mut7-C-like family of the PIN domain superfamily includes the C-terminal domain of Caenorhabditis elegans Mut-7 (also known as exonuclease 3'-5' domain-containing protein 3 homolog). Mut-7 is involved in RNA interference (RNAi) and transposon silencing in C. elegans. The Mut7-C PIN domain family is recognized as a genuine PIN domain, however it is not included it in the CDD PIN domain superfamily hierarchical model as it is lacks a core strand and helix (H3 and S3). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Other PIN domain families are: the FEN-like PIN domain family which includes the PIN domains of Flap endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and, rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains.


Pssm-ID: 350853  Cd Length: 62  Bit Score: 35.54  E-value: 8.56e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2024361882 654 VCDNMLQGLGRYLRCLGVDVRMlENEDDHRKAAEIARQEGRVILT 698
Cdd:cd18771     2 LLDVHLGTLARLLRLLGFDTAY-DNTYADATLAALADAEDRILLS 45
 
Name Accession Description Interval E-value
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
 385-597 5.19e-80

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: 256.84  E-value: 5.19e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 385 IRLLQNWEEMMQCYEKV-LKPGQIVGIDMEWRPSFGMVGKPRVSLLQLAVRDEVFLLDLPRLLeqaevKGEKEKLPHFIQ 463
Cdd:cd06146     1 IHIVDSEEELEALLLALsLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALE-----NLESEDWDRLLK 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 464 RLYSDATITKLGYGMSGDLSSLAATCSTLKGMDKQSQSVVDLLTIDKLLQKSSTDWKKGGLkvdvlspeqscedgglRQP 543
Cdd:cd06146    76 RLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNL----------------PSK 139

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2024361882 544 EKGLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCK 597
Cdd:cd06146   140 TKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 399-597 2.35e-37

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: 137.71  E-value: 2.35e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 399 EKVLKPGQIVGIDMEWRPSFGMVGKPRVSLLQLAVRDEVFLLDLPRLleqaevkgekEKLPHFIQRLYSDATITKLGYGM 478
Cdd:cd06141    12 KELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHM----------DKLPPSLKQLLEDPSILKVGVGI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 479 SGDLSSLAATCSTlkgmdkQSQSVVDLLTIDKLLQKSSTDWkkgglkvdvlspeqscedgglrqpekGLSLLVQHVLGKP 558
Cdd:cd06141    82 KGDARKLARDFGI------EVRGVVDLSHLAKRVGPRRKLV--------------------------SLARLVEEVLGLP 129

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2024361882 559 LDK--TEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCK 597
Cdd:cd06141   130 LSKpkKVRCSNWEARPLSKEQILYAATDAYASLELYRKLLA 170
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 398-595 3.44e-21

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: 91.59  E-value: 3.44e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 398 YEKVLKPGQIVGIDMEWRPSFGMVGKPRVSLLQLAVRDEVFLLDlPRLLEQAEVkgekeklpHFIQRLYSDATITKLGYG 477
Cdd:pfam01612  13 LIEELLNAPYVAVDTETTSLDTYSYYLRGALIQIGTGEGAYIID-PLALGDDVL--------SALKRLLEDPNITKVGHN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 478 MSGDLSSLAatcsTLKGMDKQSqsvvdllTIDKLLQKSstdwkkgglkvdVLSPEQScedgglrqpeKGLSLLVQHVLGK 557
Cdd:pfam01612  84 AKFDLEVLA----RDFGIKLRN-------LFDTMLAAY------------LLGYDRS----------HSLADLAEKYLGV 130

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2024361882 558 PLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKL 595
Cdd:pfam01612 131 ELDKEEQCSDWQARPLSEEQLRYAALDADYLLRLYDKL 168
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
 399-595 1.14e-20

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: 89.88  E-value: 1.14e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 399 EKVLKPGQIVGIDMEWRPSFGMvgKPRVSLLQLAVRDE-VFLLDLPRLLEQaevkgekeklPHFIQRLYSDATITKLGYG 477
Cdd:cd06129     7 EDLSMDGDVIAFDMEWPPGRRY--YGEVALIQLCVSEEkCYLFDPLSLSVD----------WQGLKMLLENPSIVKALHG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 478 MSGDLSSLaatcstLKGMDKQSQSVVDLLTIDKLLQKSSTdWkkgglkvdvlspeqscedgglrqpekGLSLLVQHVLGK 557
Cdd:cd06129    75 IEGDLWKL------LRDFGEKLQRLFDTTIAANLKGLPER-W--------------------------SLASLVEHFLGK 121

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 2024361882 558 PLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKL 595
Cdd:cd06129   122 TLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKL 159
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 399-595 4.89e-17

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: 79.71  E-value: 4.89e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882  399 EKVLKPGQIVGIDMEWRPsfGMVGKPRVSLLQLAV-RDEVFLLDLPRLLEQAEVkgekeklphfIQRLYSDATITKLGYG 477
Cdd:smart00474  15 EKLRAAGGEVALDTETTG--LDSYSGKLVLIQISVtGEGAFIIDPLALGDDLEI----------LKDLLEDETITKVGHN 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882  478 MSGDLSSLAATCSTLKGMdkqsqsvVDLLTIDKLLQKSSTDWkkgglkvdvlspeqscedgglrqpekGLSLLVQHVLGK 557
Cdd:smart00474  83 AKFDLHVLARFGIELENI-------FDTMLAAYLLLGGPSKH--------------------------GLATLLLGYLGV 129

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 2024361882  558 PLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKL 595
Cdd:smart00474 130 ELDKEEQKSDWGARPLSEEQLEYAAEDADALLRLYEKL 167
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
546-597 5.09e-14

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 74.52  E-value: 5.09e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2024361882 546 GLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCK 597
Cdd:COG0349   113 GYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYEKLLE 164
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 402-598 1.27e-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: 69.87  E-value: 1.27e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 402 LKPGQIVGIDME--WRPSFgmvgKPRVSLLQLAVRDEVFLLDLPRLLEQAEVKgekeklphfiqRLYSDATITKLGYGMS 479
Cdd:cd06142     9 LASAGVIAVDTEfmRLNTY----YPRLCLIQISTGGEVYLIDPLAIGDLSPLK-----------ELLADPNIVKVFHAAR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 480 GDLSSLAATCstlkgmDKQSQSVVDLLTIDKLLQKsstdwkkgGLKVdvlspeqscedgglrqpekGLSLLVQHVLGKPL 559
Cdd:cd06142    74 EDLELLKRDF------GILPQNLFDTQIAARLLGL--------GDSV-------------------GLAALVEELLGVEL 120

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2024361882 560 DKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCKD 598
Cdd:cd06142   121 DKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEE 159
Mut7-C pfam01927
Mut7-C RNAse domain; RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C ...
 654-748 5.42e-13

Mut7-C RNAse domain; RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C terminus.


Pssm-ID: 426515  Cd Length: 146  Bit Score: 67.28  E-value: 5.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 654 VCDNMLQGLGRYLRCLGVDVRMLENEDDhRKAAEIARQEGRVILT--SGLpyqtLRSHVGEGRCFSvnCSEKAKEQALQV 731
Cdd:pfam01927   4 LLDAMLGKLARYLRMLGYDTLYDNDYED-DELLRIAAKEGRILLTrdRGL----LKRRELTHGVYV--RSLDPEEQLREV 76

                          90
                  ....*....|....*..
gi 2024361882 732 LKHFNVHVTLADIFSRC 748
Cdd:pfam01927  77 IARLGLALSLKPEFSRC 93
DEDDy_polA_RNaseD_like_exo cd09018
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ...
 407-595 2.43e-12

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: 65.34  E-value: 2.43e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 407 IVGIDMEWRPSFGMVGKprVSLLQLAVRDEVFLLDLPRLLEQAevkgekeklPHFIQRLYSDATITKLGYGMSGDLSSLa 486
Cdd:cd09018     1 VFAFDTETDSLDNISAN--LVLIQLAIEPGVAALIPVAHDYLA---------LELLKPLLEDEKALKVGQNLKYDRGIL- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024361882 487 atcstLKGMDKQSQSVVDLLTIDKLLQKSSTDWkkgglkvdvlspeqscedgglrqpekGLSLLVQHVLGKPLDKTEQM- 565
Cdd:cd09018    69 -----LNYFIELRGIAFDTMLEAYILNSVAGRW--------------------------DMDSLVERWLGHKLIKFESIa 117

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2024361882 566 -SNWEKRPLREEQILYAASDAYCLLEVYEKL 595
Cdd:cd09018   118 gKLWFNQPLTEEQGRYAAEDADVTLQIHLKL 148
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
 540-595 2.54e-08

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: 54.91  E-value: 2.54e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2024361882 540 LRQPEKGLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKL 595
Cdd:cd06147   113 LNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRL 168
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 546-595 5.80e-08

ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. [Transcription, RNA processing]


Pssm-ID: 130455 [Multi-domain]  Cd Length: 367  Bit Score: 55.93  E-value: 5.80e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2024361882 546 GLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKL 595
Cdd:TIGR01388 113 GYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKL 162
PRK10829 PRK10829
ribonuclease D; Provisional
 546-603 1.18e-06

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 51.93  E-value: 1.18e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2024361882 546 GLSLLVQHVLGKPLDKTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCKDPESFG 603
Cdd:PRK10829  117 GFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAG 174
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 546-595 1.39e-04

bifunctional 3'-5' exonuclease/DNA polymerase; Provisional


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 45.36  E-value: 1.39e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2024361882 546 GLSLLVQHVLGKPLDKTEQMSNWEKrPLREEQILYAASDAYCLLEVYEKL 595
Cdd:PRK14975   92 SLSAAAARALGEGLDKPPQTSALSD-PPDEEQLLYAAADADVLLELYAVL 140
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 561-611 3.73e-04

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: 42.66  E-value: 3.73e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2024361882 561 KTEQMSNWEKRPLREEQILYAASDAYCLLEVYEKLCKD---PESFGLSSDLTES 611
Cdd:cd06148   139 MREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDAlisKFLKAVFKYLNTE 192
PIN_Mut7-C-like cd18771
uncharacterized subgroup of the Mut7-C-like family of the PIN domain superfamily; The ...
 654-698 8.56e-03

uncharacterized subgroup of the Mut7-C-like family of the PIN domain superfamily; The Mut7-C-like family of the PIN domain superfamily includes the C-terminal domain of Caenorhabditis elegans Mut-7 (also known as exonuclease 3'-5' domain-containing protein 3 homolog). Mut-7 is involved in RNA interference (RNAi) and transposon silencing in C. elegans. The Mut7-C PIN domain family is recognized as a genuine PIN domain, however it is not included it in the CDD PIN domain superfamily hierarchical model as it is lacks a core strand and helix (H3 and S3). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Other PIN domain families are: the FEN-like PIN domain family which includes the PIN domains of Flap endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and, rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains.


Pssm-ID: 350853  Cd Length: 62  Bit Score: 35.54  E-value: 8.56e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2024361882 654 VCDNMLQGLGRYLRCLGVDVRMlENEDDHRKAAEIARQEGRVILT 698
Cdd:cd18771     2 LLDVHLGTLARLLRLLGFDTAY-DNTYADATLAALADAEDRILLS 45
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH