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Conserved domains on  [gi|1958795163|ref|XP_038936989|]
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oligoribonuclease, mitochondrial isoform X2 [Rattus norvegicus]

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 ...
 39-103 1.65e-40

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 PRK05359:

Pssm-ID: 447876  Cd Length: 181  Bit Score: 132.20  E-value: 1.65e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958795163  39 MAQRMVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMSDWCKEHHGK 103
Cdd:PRK05359    1 NEDNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTR 65
 
Name Accession Description Interval E-value
PRK05359 PRK05359
oligoribonuclease; Provisional
 39-103 1.65e-40

oligoribonuclease; Provisional


Pssm-ID: 235429  Cd Length: 181  Bit Score: 132.20  E-value: 1.65e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958795163  39 MAQRMVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMSDWCKEHHGK 103
Cdd:PRK05359    1 NEDNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTR 65
Orn cd06135
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ...
 43-103 4.19e-40

DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. 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. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.


Pssm-ID: 99838 [Multi-domain]  Cd Length: 173  Bit Score: 131.13  E-value: 4.19e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958795163  43 MVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMSDWCKEHHGK 103
Cdd:cd06135     1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTK 61
Orn COG1949
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];
40-103 6.72e-38

Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];


Pssm-ID: 441552  Cd Length: 177  Bit Score: 125.61  E-value: 6.72e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958795163  40 AQRMVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMSDWCKEHHGK 103
Cdd:COG1949     1 DDNLVWIDLEMTGLDPETDRIIEIATIVTDSDLNILAEGPVLVIHQSDEALDGMDDWNRRMHTK 64
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 44-105 5.27e-15

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: 66.61  E-value: 5.27e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958795163  44 VWVDLEMTGLDIEKDQIIEMACLITDSDLNilAEGPNLIIKQPDELLDSMSDWCKEHHGkIT 105
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGEN--EIGETFHTYVKPTRLPKLTDECTKFTG-IT 59
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 42-105 1.93e-11

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 57.31  E-value: 1.93e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958795163   42 RMVWVDLEMTGLDIEKDQIIEMACLITDSDLniLAEGPNLIIKqPDElldSMSDWCKEHHGkIT 105
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGE--IIEVFDTYVK-PDR---PITDYATEIHG-IT 57
 
Name Accession Description Interval E-value
PRK05359 PRK05359
oligoribonuclease; Provisional
 39-103 1.65e-40

oligoribonuclease; Provisional


Pssm-ID: 235429  Cd Length: 181  Bit Score: 132.20  E-value: 1.65e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958795163  39 MAQRMVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMSDWCKEHHGK 103
Cdd:PRK05359    1 NEDNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTR 65
Orn cd06135
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ...
 43-103 4.19e-40

DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. 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. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.


Pssm-ID: 99838 [Multi-domain]  Cd Length: 173  Bit Score: 131.13  E-value: 4.19e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958795163  43 MVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMSDWCKEHHGK 103
Cdd:cd06135     1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTK 61
Orn COG1949
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];
40-103 6.72e-38

Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];


Pssm-ID: 441552  Cd Length: 177  Bit Score: 125.61  E-value: 6.72e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958795163  40 AQRMVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMSDWCKEHHGK 103
Cdd:COG1949     1 DDNLVWIDLEMTGLDPETDRIIEIATIVTDSDLNILAEGPVLVIHQSDEALDGMDDWNRRMHTK 64
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 44-105 5.27e-15

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: 66.61  E-value: 5.27e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958795163  44 VWVDLEMTGLDIEKDQIIEMACLITDSDLNilAEGPNLIIKQPDELLDSMSDWCKEHHGkIT 105
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGEN--EIGETFHTYVKPTRLPKLTDECTKFTG-IT 59
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 42-105 1.93e-11

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 57.31  E-value: 1.93e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958795163   42 RMVWVDLEMTGLDIEKDQIIEMACLITDSDLniLAEGPNLIIKqPDElldSMSDWCKEHHGkIT 105
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGE--IIEVFDTYVK-PDR---PITDYATEIHG-IT 57
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 44-74 1.07e-06

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: 44.60  E-value: 1.07e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958795163  44 VWVDLEMTGLDIEKDQIIEMACLITDSDLNI 74
Cdd:cd06127     1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEI 31
ExoI_N cd06138
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ...
 44-94 2.36e-05

N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI 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. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.


Pssm-ID: 99841 [Multi-domain]  Cd Length: 183  Bit Score: 41.10  E-value: 2.36e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958795163  44 VWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMS 94
Cdd:cd06138     1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEA 51
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 41-71 3.93e-04

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 37.89  E-value: 3.93e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958795163  41 QRMVWVDLEMTGLDIEKDQIIEMACLITDSD 71
Cdd:PRK06310    7 TEFVCLDCETTGLDVKKDRIIEFAAIRFTFD 37
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 46-67 8.24e-04

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 36.66  E-value: 8.24e-04
                          10        20
                  ....*....|....*....|..
gi 1958795163  46 VDLEMTGLDIEKDQIIEMACLI 67
Cdd:COG2176    13 FDLETTGLSPKKDEIIEIGAVK 34
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 42-67 1.29e-03

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 36.31  E-value: 1.29e-03
                          10        20
                  ....*....|....*....|....*.
gi 1958795163  42 RMVWVDLEMTGLDIEKDQIIEMACLI 67
Cdd:COG0847     1 RFVVLDTETTGLDPAKDRIIEIGAVK 26
sbcB PRK11779
exonuclease I; Provisional
 45-90 3.09e-03

exonuclease I; Provisional


Pssm-ID: 236979 [Multi-domain]  Cd Length: 476  Bit Score: 35.58  E-value: 3.09e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1958795163  45 WVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELL 90
Cdd:PRK11779   10 WHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYL 55
 
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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