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Conserved domains on  [gi|694077832|ref|WP_032423242|]
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MULTISPECIES: 3'-5' exonuclease [Klebsiella/Raoultella group]

Protein Classification

3'-5' exonuclease( domain architecture ID 11243071)

3'-5' exonuclease catalyzes the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction; belongs to the DnaQ-like (or DEDD) 3'-5' exonuclease superfamily

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 2-179 3.43e-96

3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease family. The proteins constitute a typical RNase fold, where the active site residues form a magnesium catalytic centre. The protein of the solved structure readily cleaves 3' overhangs in a time-dependent manner. It is similar to DEDD-type RNases and is an unusual ATP-binding protein that binds ATP and dATP. It forms a dimer in solution and both protomers in the asymmetric unit bind a magnesium ion through Asp-6 in SwissProt:P9WJ73. Proteins containing this domain also include 3'-5' exonuclease dexA from bacteriophage T4. It may play a role in the final step of host DNA degradation, by scavenging DNA into mononucleotides.


:

Pssm-ID: 406788  Cd Length: 177  Bit Score: 276.62  E-value: 3.43e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832    2 NHLMIDLETMGNKPAAPIVAIGAVFFAPKSSELGAEFYMAINLASAMDQGATPDGDTILWWLKQSSEARAAICTDDTRSI 81
Cdd:pfam16473   1 NHLMIDIETLGNEPTAPIVSIGAVFFDPETGELGKEFYARIDLESSMSAGATIDADTILWWLKQSSEARAQLLGDDAPSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832   82 TFALSELSSFISRHSDnPRYLKVWGNGSNFDNVILRSAYDRAGQTYPWQFWNDCDVRTMVLLGKQLGFDPKRKMPFDGVA 161
Cdd:pfam16473  81 PDALLDLNDFIRDNGD-PKSLKVWGNGASFDNVILRAAFERGGLPAPWKYWNDRDVRTIVALGPELGYDPKRDIPFEGVK 159

                         170
                  ....*....|....*...
gi 694077832  162 HNALADARHQAKYVSAIW 179
Cdd:pfam16473 160 HNALDDAIHQAKYVSAIW 177
 
Name Accession Description Interval E-value
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 2-179 3.43e-96

3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease family. The proteins constitute a typical RNase fold, where the active site residues form a magnesium catalytic centre. The protein of the solved structure readily cleaves 3' overhangs in a time-dependent manner. It is similar to DEDD-type RNases and is an unusual ATP-binding protein that binds ATP and dATP. It forms a dimer in solution and both protomers in the asymmetric unit bind a magnesium ion through Asp-6 in SwissProt:P9WJ73. Proteins containing this domain also include 3'-5' exonuclease dexA from bacteriophage T4. It may play a role in the final step of host DNA degradation, by scavenging DNA into mononucleotides.


Pssm-ID: 406788  Cd Length: 177  Bit Score: 276.62  E-value: 3.43e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832    2 NHLMIDLETMGNKPAAPIVAIGAVFFAPKSSELGAEFYMAINLASAMDQGATPDGDTILWWLKQSSEARAAICTDDTRSI 81
Cdd:pfam16473   1 NHLMIDIETLGNEPTAPIVSIGAVFFDPETGELGKEFYARIDLESSMSAGATIDADTILWWLKQSSEARAQLLGDDAPSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832   82 TFALSELSSFISRHSDnPRYLKVWGNGSNFDNVILRSAYDRAGQTYPWQFWNDCDVRTMVLLGKQLGFDPKRKMPFDGVA 161
Cdd:pfam16473  81 PDALLDLNDFIRDNGD-PKSLKVWGNGASFDNVILRAAFERGGLPAPWKYWNDRDVRTIVALGPELGYDPKRDIPFEGVK 159

                         170
                  ....*....|....*...
gi 694077832  162 HNALADARHQAKYVSAIW 179
Cdd:pfam16473 160 HNALDDAIHQAKYVSAIW 177
dexA PHA02570
exonuclease; Provisional
 4-167 7.44e-13

exonuclease; Provisional


Pssm-ID: 177399  Cd Length: 220  Bit Score: 64.32  E-value: 7.44e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832   4 LMIDLETMGNKPAAPIVAIGAVFF------APKSSELGAE-FYMAINLASAMDQgATPDGDTILWWLKQSSEARAAICT- 75
Cdd:PHA02570   4 FIIDFETFGNTPDGAVIDLAVIAFehdphnPPTFEELVSRgRRIKFDLKSQKGK-RLFDKSTIEWWKNQSPEARKNLKPs 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832  76 DDTRSITFALSELSSFISRHSDNPRYLKVWGNGSNFDNVIL----RSAYDRAGQTY--PWQFWNDCDVRTMV---LLGKQ 146
Cdd:PHA02570  83 DEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILvdviRDIHNTRDTFKlePVKFWNQRDVRTAIeatLLTRG 162

                        170       180
                 ....*....|....*....|..
gi 694077832 147 LGFDPKRKMPFDG-VAHNALAD 167
Cdd:PHA02570 163 MTTCPLPKGTLDGfVAHDSIHD 184
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 4-173 1.90e-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: 39.98  E-value: 1.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832   4 LMIDLETMGNKPAAP-IVAIGAVFFAPKSsELGAEFYMAINlasamdqgatPDGDtilwwLKQSSEARAAICTDDTR--- 79
Cdd:cd06127    1 VVFDTETTGLDPKKDrIIEIGAVKVDGGI-EIVERFETLVN----------PGRP-----IPPEATAIHGITDEMLAdap 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832  80 SITFALSELSSFISRhsdnpRYLkVwGNGSNFDNVILRSAYDRAGQTYPWQFWNDcdvrTMVLLGKQLGFDPKRKM---- 155
Cdd:cd06127   65 PFEEVLPEFLEFLGG-----RVL-V-AHNASFDLRFLNRELRRLGGPPLPNPWID----TLRLARRLLPGLRSHRLglll 133

                        170       180
                 ....*....|....*....|...
gi 694077832 156 -----PFDGVAHNALADARHQAK 173
Cdd:cd06127  134 aerygIPLEGAHRALADALATAE 156
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 110-183 4.32e-04

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 39.01  E-value: 4.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832 110 NFDNVILRSAYDRAGQTYPWQFWNDcdvrTMVLLGKQLGFDPKRK---------MPFDGvAHNALADARHQAKyvsaIWQ 180
Cdd:COG0847   89 AFDLGFLNAELRRAGLPLPPFPVLD----TLRLARRLLPGLPSYSldalcerlgIPFDE-RHRALADAEATAE----LFL 159


                 ...
gi 694077832 181 KLI 183
Cdd:COG0847  160 ALL 162
 
Name Accession Description Interval E-value
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 2-179 3.43e-96

3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease family. The proteins constitute a typical RNase fold, where the active site residues form a magnesium catalytic centre. The protein of the solved structure readily cleaves 3' overhangs in a time-dependent manner. It is similar to DEDD-type RNases and is an unusual ATP-binding protein that binds ATP and dATP. It forms a dimer in solution and both protomers in the asymmetric unit bind a magnesium ion through Asp-6 in SwissProt:P9WJ73. Proteins containing this domain also include 3'-5' exonuclease dexA from bacteriophage T4. It may play a role in the final step of host DNA degradation, by scavenging DNA into mononucleotides.


Pssm-ID: 406788  Cd Length: 177  Bit Score: 276.62  E-value: 3.43e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832    2 NHLMIDLETMGNKPAAPIVAIGAVFFAPKSSELGAEFYMAINLASAMDQGATPDGDTILWWLKQSSEARAAICTDDTRSI 81
Cdd:pfam16473   1 NHLMIDIETLGNEPTAPIVSIGAVFFDPETGELGKEFYARIDLESSMSAGATIDADTILWWLKQSSEARAQLLGDDAPSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832   82 TFALSELSSFISRHSDnPRYLKVWGNGSNFDNVILRSAYDRAGQTYPWQFWNDCDVRTMVLLGKQLGFDPKRKMPFDGVA 161
Cdd:pfam16473  81 PDALLDLNDFIRDNGD-PKSLKVWGNGASFDNVILRAAFERGGLPAPWKYWNDRDVRTIVALGPELGYDPKRDIPFEGVK 159

                         170
                  ....*....|....*...
gi 694077832  162 HNALADARHQAKYVSAIW 179
Cdd:pfam16473 160 HNALDDAIHQAKYVSAIW 177
dexA PHA02570
exonuclease; Provisional
 4-167 7.44e-13

exonuclease; Provisional


Pssm-ID: 177399  Cd Length: 220  Bit Score: 64.32  E-value: 7.44e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832   4 LMIDLETMGNKPAAPIVAIGAVFF------APKSSELGAE-FYMAINLASAMDQgATPDGDTILWWLKQSSEARAAICT- 75
Cdd:PHA02570   4 FIIDFETFGNTPDGAVIDLAVIAFehdphnPPTFEELVSRgRRIKFDLKSQKGK-RLFDKSTIEWWKNQSPEARKNLKPs 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832  76 DDTRSITFALSELSSFISRHSDNPRYLKVWGNGSNFDNVIL----RSAYDRAGQTY--PWQFWNDCDVRTMV---LLGKQ 146
Cdd:PHA02570  83 DEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILvdviRDIHNTRDTFKlePVKFWNQRDVRTAIeatLLTRG 162

                        170       180
                 ....*....|....*....|..
gi 694077832 147 LGFDPKRKMPFDG-VAHNALAD 167
Cdd:PHA02570 163 MTTCPLPKGTLDGfVAHDSIHD 184
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 4-173 1.90e-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: 39.98  E-value: 1.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832   4 LMIDLETMGNKPAAP-IVAIGAVFFAPKSsELGAEFYMAINlasamdqgatPDGDtilwwLKQSSEARAAICTDDTR--- 79
Cdd:cd06127    1 VVFDTETTGLDPKKDrIIEIGAVKVDGGI-EIVERFETLVN----------PGRP-----IPPEATAIHGITDEMLAdap 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832  80 SITFALSELSSFISRhsdnpRYLkVwGNGSNFDNVILRSAYDRAGQTYPWQFWNDcdvrTMVLLGKQLGFDPKRKM---- 155
Cdd:cd06127   65 PFEEVLPEFLEFLGG-----RVL-V-AHNASFDLRFLNRELRRLGGPPLPNPWID----TLRLARRLLPGLRSHRLglll 133

                        170       180
                 ....*....|....*....|...
gi 694077832 156 -----PFDGVAHNALADARHQAK 173
Cdd:cd06127  134 aerygIPLEGAHRALADALATAE 156
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 110-183 4.32e-04

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 39.01  E-value: 4.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832 110 NFDNVILRSAYDRAGQTYPWQFWNDcdvrTMVLLGKQLGFDPKRK---------MPFDGvAHNALADARHQAKyvsaIWQ 180
Cdd:COG0847   89 AFDLGFLNAELRRAGLPLPPFPVLD----TLRLARRLLPGLPSYSldalcerlgIPFDE-RHRALADAEATAE----LFL 159


                 ...
gi 694077832 181 KLI 183
Cdd:COG0847  160 ALL 162
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 81-175 5.69e-03

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These 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. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 36.04  E-value: 5.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694077832  81 ITF--ALSELSSFISRHSDNPRYlkVWGNGSnfDNVILRSAYDRAGQTYPWQFWNDCDVRTMVLlgKQLGFDPKRKM--- 155
Cdd:cd06133   73 PSFpeVLKEFLEWLGKNGKYAFV--TWGDWD--LKDLLQNQCKYKIINLPPFFRQWIDLKKEFA--KFYGLKKRTGLska 146

                         90       100
                 ....*....|....*....|....*.
gi 694077832 156 ------PFDGVAHNALADARHQAKYV 175
Cdd:cd06133  147 leylglEFEGRHHRGLDDARNIARIL 172
 
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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