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Conserved domains on  [gi|735367247|ref|NP_001290164|]
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interferon-stimulated gene 20 kDa protein isoform b [Homo sapiens]

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
SCOP:  4000547

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 ...
 64-152 2.28e-46

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: 148.74  E-value: 2.28e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  64 GQILQLLKGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVED 143
Cdd:cd06149   69 KEILKILKGKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVED 148


                 ....*....
gi 735367247 144 ARATMELYQ 152
Cdd:cd06149  149 ARATMELYK 157
 
Name Accession Description Interval E-value
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 64-152 2.28e-46

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: 148.74  E-value: 2.28e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  64 GQILQLLKGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVED 143
Cdd:cd06149   69 KEILKILKGKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVED 148


                 ....*....
gi 735367247 144 ARATMELYQ 152
Cdd:cd06149  149 ARATMELYK 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 65-152 2.82e-17

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 74.64  E-value: 2.82e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247    65 QILQLLKGK-LVVGHDLKHDFQALKEDMSGYTIYDTST----DRLLWREAKLDHCRRVSLRVLSERLLHKSIQNsllGHS 139
Cdd:smart00479  73 ELLEFLRGRiLVAGNSAHFDLRFLKLEHPRLGIKQPPKlpviDTLKLARATNPGLPKYSLKKLAKRLLLEVIQR---AHR 149

                           90
                   ....*....|...
gi 735367247   140 SVEDARATMELYQ 152
Cdd:smart00479 150 ALDDARATAKLFK 162
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 65-152 6.42e-06

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 44.01  E-value: 6.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  65 QILQLLKGKLVVGHD-------LKHDFQALKEDMSGYTIYDTST-DRLLWREAKldhcrRVSLRVLSERLlHKSIQNSll 136
Cdd:COG0847   73 ELLEFLGGAVLVAHNaafdlgfLNAELRRAGLPLPPFPVLDTLRlARRLLPGLP-----SYSLDALCERL-GIPFDER-- 144

                         90
                 ....*....|....*.
gi 735367247 137 gHSSVEDARATMELYQ 152
Cdd:COG0847  145 -HRALADAEATAELFL 159
 
Name Accession Description Interval E-value
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 64-152 2.28e-46

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: 148.74  E-value: 2.28e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  64 GQILQLLKGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSLLGHSSVED 143
Cdd:cd06149   69 KEILKILKGKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVED 148


                 ....*....
gi 735367247 144 ARATMELYQ 152
Cdd:cd06149  149 ARATMELYK 157
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 65-152 2.94e-30

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: 107.60  E-value: 2.94e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  65 QILQLLKGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKldhCRRVSLRVLSERLLHKSIQNSllGHSSVEDA 144
Cdd:cd06144   70 KVAELLKGRILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAK---GKSPSLKKLAKQLLGLDIQEG--EHSSVEDA 144


                 ....*...
gi 735367247 145 RATMELYQ 152
Cdd:cd06144  145 RAAMRLYR 152
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 52-152 6.82e-24

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: 91.57  E-value: 6.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  52 MLGHVGVGTCLPG------QILQLLKGK-LVVGHDLKHDFQALKedMSGYTIYDTSTDRLLWREAKLDhCRRVSLRVLSE 124
Cdd:cd06137   57 LEEAAKAGKTIFGweaaraALWKFIDPDtILVGHSLQNDLDALR--MIHTRVVDTAILTREAVKGPLA-KRQWSLRTLCR 133

                         90       100
                 ....*....|....*....|....*...
gi 735367247 125 RLLHKSIQNSLLGHSSVEDARATMELYQ 152
Cdd:cd06137  134 DFLGLKIQGGGEGHDSLEDALAAREVVL 161
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 65-152 2.82e-17

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 74.64  E-value: 2.82e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247    65 QILQLLKGK-LVVGHDLKHDFQALKEDMSGYTIYDTST----DRLLWREAKLDHCRRVSLRVLSERLLHKSIQNsllGHS 139
Cdd:smart00479  73 ELLEFLRGRiLVAGNSAHFDLRFLKLEHPRLGIKQPPKlpviDTLKLARATNPGLPKYSLKKLAKRLLLEVIQR---AHR 149

                           90
                   ....*....|...
gi 735367247   140 SVEDARATMELYQ 152
Cdd:smart00479 150 ALDDARATAKLFK 162
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 49-150 1.01e-15

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: 69.82  E-value: 1.01e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  49 TQKMLghVGVGTCLPG---QILQLL-KGKLVVGHDLKHDFQALKedMSGYTIYDTStdrLLWReakldHCR----RVSLR 120
Cdd:cd06145   51 TEEML--ENVTTTLEDvqkKLLSLIsPDTILVGHSLENDLKALK--LIHPRVIDTA---ILFP-----HPRgppyKPSLK 118

                         90       100       110
                 ....*....|....*....|....*....|
gi 735367247 121 VLSERLLHKSIQNSLLGHSSVEDARATMEL 150
Cdd:cd06145  119 NLAKKYLGRDIQQGEGGHDSVEDARAALEL 148
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 67-152 2.67e-08

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: 50.69  E-value: 2.67e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  67 LQLL--KGKLVVGHDLKHDFQALKEDMSGYTIYDTSTdrLLWREAKldhcRRVSLRVLSERLLHKSIQNSllGHSSVEDA 144
Cdd:cd06143   95 LRLLvdLGCIFVGHGLAKDFRVINIQVPKEQVIDTVE--LFHLPGQ----RKLSLRFLAWYLLGEKIQSE--THDSIEDA 166


                 ....*...
gi 735367247 145 RATMELYQ 152
Cdd:cd06143  167 RTALKLYR 174
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 65-152 6.42e-06

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 44.01  E-value: 6.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  65 QILQLLKGKLVVGHD-------LKHDFQALKEDMSGYTIYDTST-DRLLWREAKldhcrRVSLRVLSERLlHKSIQNSll 136
Cdd:COG0847   73 ELLEFLGGAVLVAHNaafdlgfLNAELRRAGLPLPPFPVLDTLRlARRLLPGLP-----SYSLDALCERL-GIPFDER-- 144

                         90
                 ....*....|....*.
gi 735367247 137 gHSSVEDARATMELYQ 152
Cdd:COG0847  145 -HRALADAEATAELFL 159
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 65-152 9.52e-04

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: 37.67  E-value: 9.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 735367247  65 QILQLLKGKLVVGHD-------LKHDFQALKEDMSGYTIYDTST-DRLLWRE---AKLDHCRRVSLRVLSERllhksiqn 133
Cdd:cd06127   72 EFLEFLGGRVLVAHNasfdlrfLNRELRRLGGPPLPNPWIDTLRlARRLLPGlrsHRLGLLLAERYGIPLEG-------- 143

                         90
                 ....*....|....*....
gi 735367247 134 sllGHSSVEDARATMELYQ 152
Cdd:cd06127  144 ---AHRALADALATAELLL 159
 
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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