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Conserved domains on  [gi|600971674|ref|NP_001278150|]
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interferon-stimulated gene 20 kDa protein isoform b [Mus musculus]

Protein Classification

3'-5' exonuclease family protein( domain architecture ID 1085)

3'-5' exonuclease family protein may cleave nucleotides one at a time from the end (exo) of a polynucleotide chain

CATH:  3.30.420.10
Gene Ontology:  GO:0003676
PubMed:  11988770|11222749

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaQ_like_exo super family cl10012
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 8-163 2.10e-89

DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which 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 patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.


The actual alignment was detected with superfamily member cd06149:

Pssm-ID: 447876  Cd Length: 157  Bit Score: 258.14  E-value: 2.10e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   8 VAMDCEMVGLGPQ-RVSGLARCSIVNIHGAVLYDKYIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLV 86
Cdd:cd06149    1 VAIDCEMVGTGPGgRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 600971674  87 VGHDLKHDFNALKEDMSKYTIYDTSTDRLLWHEAKLQYYSRVSLRLLCKRLLHKNIQNNWRGHCSVEDARATMELYK 163
Cdd:cd06149   81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157
 
Name Accession Description Interval E-value
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 8-163 2.10e-89

DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved 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. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.


Pssm-ID: 99852  Cd Length: 157  Bit Score: 258.14  E-value: 2.10e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   8 VAMDCEMVGLGPQ-RVSGLARCSIVNIHGAVLYDKYIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLV 86
Cdd:cd06149    1 VAIDCEMVGTGPGgRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 600971674  87 VGHDLKHDFNALKEDMSKYTIYDTSTDRLLWHEAKLQYYSRVSLRLLCKRLLHKNIQNNWRGHCSVEDARATMELYK 163
Cdd:cd06149   81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 6-163 3.11e-44

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 144.37  E-value: 3.11e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674     6 EVVAMDCEMVGLGPQrVSGLARCSIVNIHG---AVLYDKYIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLK 82
Cdd:smart00479   1 TLVVIDCETTGLDPG-KDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674    83 GK-LVVGHDLKHDFNALKEDMSKYTIYDTST----DRLLWHEAKLQYYSRVSLRLLCKRLLHKNIQnnwRGHCSVEDARA 157
Cdd:smart00479  80 GRiLVAGNSAHFDLRFLKLEHPRLGIKQPPKlpviDTLKLARATNPGLPKYSLKKLAKRLLLEVIQ---RAHRALDDARA 156


                   ....*.
gi 600971674   158 TMELYK 163
Cdd:smart00479 157 TAKLFK 162
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 8-162 1.02e-19

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 81.24  E-value: 1.02e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674    8 VAMDCEMVGLGPQ--RVSGLARCSIVN--IHGAVLYDKYIRPE--GEITDYRTQVSGVTPQHMVRATPFGEARLEILQLL 81
Cdd:pfam00929   1 VVIDLETTGLDPEkdEIIEIAAVVIDGgeNEIGETFHTYVKPTrlPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   82 -KGKLVVGHDLKHDFNALKEDMSKYTIYDTSTDRLLWHE-----AKLQYYSRVSLRLLCKRLLHKNIQnnwRGHCSVEDA 155
Cdd:pfam00929  81 rKGNLLVAHNASFDVGFLRYDDKRFLKKPMPKLNPVIDTlildkATYKELPGRSLDALAEKLGLEHIG---RAHRALDDA 157


                  ....*..
gi 600971674  156 RATMELY 162
Cdd:pfam00929 158 RATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 6-162 1.30e-18

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 78.30  E-value: 1.30e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   6 EVVAMDCEMVGLGPQRvsglarCSIVNIhGAVLYDK---------YIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLE 76
Cdd:COG0847    1 RFVVLDTETTGLDPAK------DRIIEI-GAVKVDDgrivetfhtLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674  77 ILQLLKGKLVVGHD-------LKHDFNALKEDMSKYTIYDTST-DRLLWHEAKlqyysRVSLRLLCKRLlhkNIQNNWRg 148
Cdd:COG0847   74 LLEFLGGAVLVAHNaafdlgfLNAELRRAGLPLPPFPVLDTLRlARRLLPGLP-----SYSLDALCERL---GIPFDER- 144

                        170
                 ....*....|....
gi 600971674 149 HCSVEDARATMELY 162
Cdd:COG0847  145 HRALADAEATAELF 158
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 30-166 9.37e-05

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 41.98  E-value: 9.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674  30 IVNIHGAVLYDKY---IRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLVVGHDLKHDFNALKEDMSkYT 106
Cdd:PRK07246  30 IVIIEGGEIIDSYttdVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDCIFVAHNVKFDANLLAEALF-LE 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 600971674 107 IYDTSTDRLLWHE-AKLQY--YSRVSLRLLCkRLLHKNIQNnwrGHCSVEDARATMELY-----KISQ 166
Cdd:PRK07246 109 GYELRTPRVDTVElAQVFFptLEKYSLSHLS-RELNIDLAD---AHTAIADARATAELFlkllqKIES 172
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 42-163 3.10e-03

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 37.04  E-value: 3.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   42 YIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLVVGHDLKHDFNALKEDMSKYTIYDTSTDRLLWHEAK 121
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDT 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 600971674  122 LQYY------SRVSLRLLCKRLlhkNIQNNWRG-HCSVEDARATMELYK 163
Cdd:TIGR00573 126 LQYArpefpgKRNTLDALCKRY---EITNSHRAlHGALADAFILAKLYL 171
 
Name Accession Description Interval E-value
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 8-163 2.10e-89

DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved 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. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.


Pssm-ID: 99852  Cd Length: 157  Bit Score: 258.14  E-value: 2.10e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   8 VAMDCEMVGLGPQ-RVSGLARCSIVNIHGAVLYDKYIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLV 86
Cdd:cd06149    1 VAIDCEMVGTGPGgRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 600971674  87 VGHDLKHDFNALKEDMSKYTIYDTSTDRLLWHEAKLQYYSRVSLRLLCKRLLHKNIQNNWRGHCSVEDARATMELYK 163
Cdd:cd06149   81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 8-163 2.36e-73

DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved 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. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.


Pssm-ID: 99847  Cd Length: 152  Bit Score: 217.38  E-value: 2.36e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   8 VAMDCEMVGLGP-QRVSGLARCSIVNIHGAVLYDKYIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLV 86
Cdd:cd06144    1 VALDCEMVGVGPdGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 600971674  87 VGHDLKHDFNALKEDMSKYTIYDTSTDRLLWHEAKLQyysRVSLRLLCKRLLHKNIQNnwRGHCSVEDARATMELYK 163
Cdd:cd06144   81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGK---SPSLKKLAKQLLGLDIQE--GEHSSVEDARAAMRLYR 152
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 8-162 5.36e-50

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved 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. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.


Pssm-ID: 99840  Cd Length: 161  Bit Score: 158.60  E-value: 5.36e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   8 VAMDCEMVGLGPQRvSGLARCSIVN-IHGAVLYDKYIRPEGEITDYRTQVSGVTPQHMVRA-----TPFG--EARLEILQ 79
Cdd:cd06137    1 VALDCEMVGLADGD-SEVVRISAVDvLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAakagkTIFGweAARAALWK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674  80 LLKGK-LVVGHDLKHDFNALKedMSKYTIYDTSTDRLLWHEAKLQyYSRVSLRLLCKRLLHKNIQNNWRGHCSVEDARAT 158
Cdd:cd06137   80 FIDPDtILVGHSLQNDLDALR--MIHTRVVDTAILTREAVKGPLA-KRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAA 156


                 ....
gi 600971674 159 MELY 162
Cdd:cd06137  157 REVV 160
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 8-161 2.38e-46

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 148.79  E-value: 2.38e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   8 VAMDCEMV--GLGpqrvSGLARCSIVNIHGAVLYDKYIRPEGEITDYRTQVSGVTPQHMVRATP-FGEARLEILQLL-KG 83
Cdd:cd06145    1 FALDCEMCytTDG----LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTtLEDVQKKLLSLIsPD 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 600971674  84 KLVVGHDLKHDFNALKedMSKYTIYDTStdrLLWHeAKLQYYSRVSLRLLCKRLLHKNIQNNWRGHCSVEDARATMEL 161
Cdd:cd06145   77 TILVGHSLENDLKALK--LIHPRVIDTA---ILFP-HPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALEL 148
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 6-163 3.11e-44

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 144.37  E-value: 3.11e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674     6 EVVAMDCEMVGLGPQrVSGLARCSIVNIHG---AVLYDKYIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLK 82
Cdd:smart00479   1 TLVVIDCETTGLDPG-KDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674    83 GK-LVVGHDLKHDFNALKEDMSKYTIYDTST----DRLLWHEAKLQYYSRVSLRLLCKRLLHKNIQnnwRGHCSVEDARA 157
Cdd:smart00479  80 GRiLVAGNSAHFDLRFLKLEHPRLGIKQPPKlpviDTLKLARATNPGLPKYSLKKLAKRLLLEVIQ---RAHRALDDARA 156


                   ....*.
gi 600971674   158 TMELYK 163
Cdd:smart00479 157 TAKLFK 162
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 8-162 1.02e-19

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 81.24  E-value: 1.02e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674    8 VAMDCEMVGLGPQ--RVSGLARCSIVN--IHGAVLYDKYIRPE--GEITDYRTQVSGVTPQHMVRATPFGEARLEILQLL 81
Cdd:pfam00929   1 VVIDLETTGLDPEkdEIIEIAAVVIDGgeNEIGETFHTYVKPTrlPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   82 -KGKLVVGHDLKHDFNALKEDMSKYTIYDTSTDRLLWHE-----AKLQYYSRVSLRLLCKRLLHKNIQnnwRGHCSVEDA 155
Cdd:pfam00929  81 rKGNLLVAHNASFDVGFLRYDDKRFLKKPMPKLNPVIDTlildkATYKELPGRSLDALAEKLGLEHIG---RAHRALDDA 157


                  ....*..
gi 600971674  156 RATMELY 162
Cdd:pfam00929 158 RATAKLF 164
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 8-163 5.78e-19

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved 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: 99846  Cd Length: 174  Bit Score: 79.20  E-value: 5.78e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   8 VAMDCEMVGLGP---------------QRVSGLARCSIV----NIHGAVLYDKYIRPEGEITDYRTQVSGVTP------- 61
Cdd:cd06143    1 VAIDAEFVKLKPeeteirsdgtkstirPSQMSLARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPgdldpkt 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674  62 -QHMVraTPFGEARLEiLQLL--KGKLVVGHDLKHDFNALKEDMSKYTIYDTSTdrLLWHEAKlqyySRVSLRLLCKRLL 138
Cdd:cd06143   81 sSKNL--TTLKSAYLK-LRLLvdLGCIFVGHGLAKDFRVINIQVPKEQVIDTVE--LFHLPGQ----RKLSLRFLAWYLL 151

                        170       180
                 ....*....|....*....|....*
gi 600971674 139 HKNIQNNwrGHCSVEDARATMELYK 163
Cdd:cd06143  152 GEKIQSE--THDSIEDARTALKLYR 174
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 8-163 6.12e-19

DEDDh 3'-5' exonuclease domain family; DEDDh 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. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 78.88  E-value: 6.12e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   8 VAMDCEMVGLGPQRvsglarCSIVNIhGAVL----------YDKYIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEI 77
Cdd:cd06127    1 VVFDTETTGLDPKK------DRIIEI-GAVKvdggieiverFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEF 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674  78 LQLLKGKLVVGHDLKHDFNALKEDMSKYTIYDTSTDRL-LWHEAKLQYYSRVSLRLLCKRLLHKNIqNNWRGHCSVEDAR 156
Cdd:cd06127   74 LEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIdTLRLARRLLPGLRSHRLGLLLAERYGI-PLEGAHRALADAL 152


                 ....*..
gi 600971674 157 ATMELYK 163
Cdd:cd06127  153 ATAELLL 159
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 6-162 1.30e-18

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 78.30  E-value: 1.30e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   6 EVVAMDCEMVGLGPQRvsglarCSIVNIhGAVLYDK---------YIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLE 76
Cdd:COG0847    1 RFVVLDTETTGLDPAK------DRIIEI-GAVKVDDgrivetfhtLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674  77 ILQLLKGKLVVGHD-------LKHDFNALKEDMSKYTIYDTST-DRLLWHEAKlqyysRVSLRLLCKRLlhkNIQNNWRg 148
Cdd:COG0847   74 LLEFLGGAVLVAHNaafdlgfLNAELRRAGLPLPPFPVLDTLRlARRLLPGLP-----SYSLDALCERL---GIPFDER- 144

                        170
                 ....*....|....
gi 600971674 149 HCSVEDARATMELY 162
Cdd:COG0847  145 HRALADAEATAELF 158
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 28-162 3.81e-09

an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved 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. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99834 [Multi-domain]  Cd Length: 156  Bit Score: 52.90  E-value: 3.81e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674  28 CSI--VNIHGAVLYDKY---IRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLVVGHDLKHDFNALKEDM 102
Cdd:cd06130   17 CSIglVKVRDGQIVDTFytlIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAAL 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 600971674 103 SKytiYDTSTDRLLWHE----AKLQYYSRVSLRL--LCKRLlhkNIqnNWRGHCSVEDARATMELY 162
Cdd:cd06130   97 EA---YGLPPPPYQYLCtvrlARRVWPLLPNHKLntVAEHL---GI--ELNHHDALEDARACAEIL 154
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 30-166 9.37e-05

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 41.98  E-value: 9.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674  30 IVNIHGAVLYDKY---IRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLVVGHDLKHDFNALKEDMSkYT 106
Cdd:PRK07246  30 IVIIEGGEIIDSYttdVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDCIFVAHNVKFDANLLAEALF-LE 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 600971674 107 IYDTSTDRLLWHE-AKLQY--YSRVSLRLLCkRLLHKNIQNnwrGHCSVEDARATMELY-----KISQ 166
Cdd:PRK07246 109 GYELRTPRVDTVElAQVFFptLEKYSLSHLS-RELNIDLAD---AHTAIADARATAELFlkllqKIES 172
polC PRK00448
DNA polymerase III PolC; Validated
 39-174 9.68e-05

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 42.13  E-value: 9.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   39 YDKYIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLVVGHDLKHDFNALKE-------DMSKYTIYDT- 110
Cdd:PRK00448  455 FEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTnyeklglEKIKNPVIDTl 534

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 600971674  111 --StdRLLWHEAKlqyysRVSLRLLCKRLlhkNIQNNwRGHCSVEDARATMELYKISQRLRAQRGL 174
Cdd:PRK00448  535 elS--RFLYPELK-----SHRLNTLAKKF---GVELE-HHHRADYDAEATAYLLIKFLKDLKEKGI 589
PRK07740 PRK07740
hypothetical protein; Provisional
 1-176 1.53e-03

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 38.11  E-value: 1.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   1 MAGIP----EVVAMDCEMVGLGPQRVSGLARCSIVNIHGA-VLYDKY---IRPEGEITDYRTQVSGVTPQHMVRATPFGE 72
Cdd:PRK07740  51 VLDIPltdlPFVVFDLETTGFSPQQGDEILSIGAVKTKGGeVETDTFyslVKPKRPIPEHILELTGITAEDVAFAPPLAE 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674  73 ARLEILQLLKGKLVVGHDLKHDFNALKEdmskytiydtstdrLLWHEAKLQYYSRV-SLRLLCKRLLHK----------- 140
Cdd:PRK07740 131 VLHRFYAFIGAGVLVAHHAGHDKAFLRH--------------ALWRTYRQPFTHRLiDTMFLTKLLAHErdfptlddala 196

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 600971674 141 --NIQNNWRgHCSVEDARATMELYKISQRLRAQRGLPC 176
Cdd:PRK07740 197 yyGIPIPRR-HHALGDALMTAKLWAILLVEAQQRGITT 233
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 42-163 3.10e-03

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 37.04  E-value: 3.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 600971674   42 YIRPEGEITDYRTQVSGVTPQHMVRATPFGEARLEILQLLKGKLVVGHDLKHDFNALKEDMSKYTIYDTSTDRLLWHEAK 121
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDT 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 600971674  122 LQYY------SRVSLRLLCKRLlhkNIQNNWRG-HCSVEDARATMELYK 163
Cdd:TIGR00573 126 LQYArpefpgKRNTLDALCKRY---EITNSHRAlHGALADAFILAKLYL 171
 
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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