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Conserved domains on  [gi|19113423|ref|NP_596631|]
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exoribonuclease Rex4 [Schizosaccharomyces pombe]

Protein Classification

RNA exonuclease 4( domain architecture ID 10150217)

RNA exonuclease 4 is a DEDDh-type DnaQ-like 3'-5' exonuclease that functions in the processing and maturation of many RNA species

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676|GO:0006364|GO:0006281
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 94-243 4.96e-96

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: 278.25  E-value: 4.96e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  94 IAMDCEMVGVADD--MSVLARVSIVNYHGHVVYDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKILDNRVL 171
Cdd:cd06144   1 VALDCEMVGVGPDgsESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19113423 172 VGHAVHNDLKVLLLSHPRRMIRDTSRFSGYRKLAKGRTPGLKKLAEVILGRDIQSGQHSSVQDAQATMELYK 243
Cdd:cd06144  81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 94-243 4.96e-96

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: 278.25  E-value: 4.96e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  94 IAMDCEMVGVADD--MSVLARVSIVNYHGHVVYDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKILDNRVL 171
Cdd:cd06144   1 VALDCEMVGVGPDgsESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19113423 172 VGHAVHNDLKVLLLSHPRRMIRDTSRFSGYRKLAKGRTPGLKKLAEVILGRDIQSGQHSSVQDAQATMELYK 243
Cdd:cd06144  81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 92-249 1.66e-45

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 150.14  E-value: 1.66e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423     92 KYIAMDCEMVGVADDMSVLARVSIVNYHG---HVVYDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKILDN 168
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423    169 RVLV-GHAVHNDLKVLLLSHPR--------RMIRDTSRFSGYRKLAKGRTpGLKKLAEVILGRDIQSGqHSSVQDAQATM 239
Cdd:smart00479  81 RILVaGNSAHFDLRFLKLEHPRlgikqppkLPVIDTLKLARATNPGLPKY-SLKKLAKRLLLEVIQRA-HRALDDARATA 158

                          170
                   ....*....|
gi 19113423    240 ELYKKVKKEM 249
Cdd:smart00479 159 KLFKKLLERL 168
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 94-242 2.59e-18

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: 79.32  E-value: 2.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423    94 IAMDCEMVGVA---DDMSVLARVSIVNY--HGHVVYDTYVRPKE--KVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKIL 166
Cdd:pfam00929   1 VVIDLETTGLDpekDEIIEIAAVVIDGGenEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423   167 D---------NRVLVGHAVHNDLKVLLLSHPRRM-IRDTSRFSgYRKLAKGRTPGLKKLAEVILGRDIQSgQHSSVQDAQ 236
Cdd:pfam00929  81 RkgnllvahnASFDVGFLRYDDKRFLKKPMPKLNpVIDTLILD-KATYKELPGRSLDALAEKLGLEHIGR-AHRALDDAR 158


                  ....*.
gi 19113423   237 ATMELY 242
Cdd:pfam00929 159 ATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 92-244 3.47e-15

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 70.98  E-value: 3.47e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  92 KYIAMDCEMVG--VADDmSVLArVSIVNYHGHVV---YDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKIL 166
Cdd:COG0847   1 RFVVLDTETTGldPAKD-RIIE-IGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423 167 DNRVLVGHAVHNDLKVL-------LLSHPRRMIRDTSRfsgyrkLAKGRTPGLK--KLAEVI--LGRDIqSGQHSSVQDA 235
Cdd:COG0847  79 GGAVLVAHNAAFDLGFLnaelrraGLPLPPFPVLDTLR------LARRLLPGLPsySLDALCerLGIPF-DERHRALADA 151


                ....*....
gi 19113423 236 QATMELYKK 244
Cdd:COG0847 152 EATAELFLA 160
PRK07247 PRK07247
3'-5' exonuclease;
87-244 1.57e-06

3'-5' exonuclease;


Pssm-ID: 180906 [Multi-domain]  Cd Length: 195  Bit Score: 47.47  E-value: 1.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423   87 LETLGKYIAMDCEMVGVaDDMSVLARVSIVNYHGHV---VYDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVA 163
Cdd:PRK07247   1 MKRLETYIAFDLEFNTV-NGVSHIIQVSAVKYDDHKevdSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  164 KILDNRVLVGH-AVHNDLKVL------LLSHPRRMIRDTS---RFSGYRKLAKGRtpgLKKLAEvILGrdIQSGQHSSVQ 233
Cdd:PRK07247  80 EFVGELPLIGYnAQKSDLPILaengldLSDQYQVDLYDEAferRSSDLNGIANLK---LQTVAD-FLG--IKGRGHNSLE 153

                        170
                 ....*....|.
gi 19113423  234 DAQATMELYKK 244
Cdd:PRK07247 154 DARMTARVYES 164
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 94-243 4.96e-96

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: 278.25  E-value: 4.96e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  94 IAMDCEMVGVADD--MSVLARVSIVNYHGHVVYDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKILDNRVL 171
Cdd:cd06144   1 VALDCEMVGVGPDgsESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19113423 172 VGHAVHNDLKVLLLSHPRRMIRDTSRFSGYRKLAKGRTPGLKKLAEVILGRDIQSGQHSSVQDAQATMELYK 243
Cdd:cd06144  81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 94-243 3.46e-58

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: 182.25  E-value: 3.46e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  94 IAMDCEMVGVADD--MSVLARVSIVNYHGHVVYDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKILDNRVL 171
Cdd:cd06149   1 VAIDCEMVGTGPGgrESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19113423 172 VGHAVHNDLKVLLLSHPRRMIRDTSRFSGYRKLAK---GRTPGLKKLAEVILGRDIQSGQ--HSSVQDAQATMELYK 243
Cdd:cd06149  81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGfpeNCRVSLKVLAKRLLHRDIQVGRqgHSSVEDARATMELYK 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 92-249 1.66e-45

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 150.14  E-value: 1.66e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423     92 KYIAMDCEMVGVADDMSVLARVSIVNYHG---HVVYDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKILDN 168
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGgeiIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423    169 RVLV-GHAVHNDLKVLLLSHPR--------RMIRDTSRFSGYRKLAKGRTpGLKKLAEVILGRDIQSGqHSSVQDAQATM 239
Cdd:smart00479  81 RILVaGNSAHFDLRFLKLEHPRlgikqppkLPVIDTLKLARATNPGLPKY-SLKKLAKRLLLEVIQRA-HRALDDARATA 158

                          170
                   ....*....|
gi 19113423    240 ELYKKVKKEM 249
Cdd:smart00479 159 KLFKKLLERL 168
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 94-243 1.93e-45

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: 149.56  E-value: 1.93e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  94 IAMDCEMVGVADDMsVLARVSIVNYHGHVVYDTYVRPKEKVTDWRTWVSGVKSFHMRDAP-SFEKVQAEVAKILD-NRVL 171
Cdd:cd06145   1 FALDCEMCYTTDGL-ELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTtTLEDVQKKLLSLISpDTIL 79

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19113423 172 VGHAVHNDLKVLLLSHPRrmIRDTS----RFSGYRKlakgrTPGLKKLAEVILGRDIQSGQ--HSSVQDAQATMELYK 243
Cdd:cd06145  80 VGHSLENDLKALKLIHPR--VIDTAilfpHPRGPPY-----KPSLKNLAKKYLGRDIQQGEggHDSVEDARAALELVK 150
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 94-242 4.36e-38

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: 130.86  E-value: 4.36e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  94 IAMDCEMVGVADDMSVLARVSIVNY-HGHVVYDTYVRPKEKVTDWRTWVSGVKSFHMRDA-------PSFEKVQAEVAKI 165
Cdd:cd06137   1 VALDCEMVGLADGDSEVVRISAVDVlTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAakagktiFGWEAARAALWKF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423 166 LDNR-VLVGHAVHNDLKVLLLSHPRrmIRDTSR-FSGYRKLAK-GRTPGLKKLAEVILGRDIQSGQ--HSSVQDAQATME 240
Cdd:cd06137  81 IDPDtILVGHSLQNDLDALRMIHTR--VVDTAIlTREAVKGPLaKRQWSLRTLCRDFLGLKIQGGGegHDSLEDALAARE 158


                ..
gi 19113423 241 LY 242
Cdd:cd06137 159 VV 160
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 94-242 2.59e-18

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: 79.32  E-value: 2.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423    94 IAMDCEMVGVA---DDMSVLARVSIVNY--HGHVVYDTYVRPKE--KVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKIL 166
Cdd:pfam00929   1 VVIDLETTGLDpekDEIIEIAAVVIDGGenEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423   167 D---------NRVLVGHAVHNDLKVLLLSHPRRM-IRDTSRFSgYRKLAKGRTPGLKKLAEVILGRDIQSgQHSSVQDAQ 236
Cdd:pfam00929  81 RkgnllvahnASFDVGFLRYDDKRFLKKPMPKLNpVIDTLILD-KATYKELPGRSLDALAEKLGLEHIGR-AHRALDDAR 158


                  ....*.
gi 19113423   237 ATMELY 242
Cdd:pfam00929 159 ATAKLF 164
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 110-243 5.50e-17

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: 76.12  E-value: 5.50e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423 110 LARVSIV----NYHGHVVYDTYVRPKEKVTDWRTWVSGVKSFHMrDAPSFEK--VQAEVA----KILDNR--VLVGHAVH 177
Cdd:cd06143  33 LARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDL-DPKTSSKnlTTLKSAylklRLLVDLgcIFVGHGLA 111

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19113423 178 NDLKVLLLSHPRRMIRDTS---RFSGYRKLAkgrtpgLKKLAEVILGRDIQSGQHSSVQDAQATMELYK 243
Cdd:cd06143 112 KDFRVINIQVPKEQVIDTVelfHLPGQRKLS------LRFLAWYLLGEKIQSETHDSIEDARTALKLYR 174
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 92-244 3.47e-15

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 70.98  E-value: 3.47e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  92 KYIAMDCEMVG--VADDmSVLArVSIVNYHGHVV---YDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKIL 166
Cdd:COG0847   1 RFVVLDTETTGldPAKD-RIIE-IGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423 167 DNRVLVGHAVHNDLKVL-------LLSHPRRMIRDTSRfsgyrkLAKGRTPGLK--KLAEVI--LGRDIqSGQHSSVQDA 235
Cdd:COG0847  79 GGAVLVAHNAAFDLGFLnaelrraGLPLPPFPVLDTLR------LARRLLPGLPsySLDALCerLGIPF-DERHRALADA 151


                ....*....
gi 19113423 236 QATMELYKK 244
Cdd:COG0847 152 EATAELFLA 160
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 94-243 4.75e-13

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: 65.01  E-value: 4.75e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  94 IAMDCEMVGVADDMSVLARVSIVNYHGHVV----YDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKILDNR 169
Cdd:cd06127   1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEiverFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423 170 VLVGHAVHNDLKVL-------LLSHPRRMIRDTSRFsgYRKLAKGRTPGLKKLAEVILGRDIQSGQHSSVQDAQATMELY 242
Cdd:cd06127  81 VLVAHNASFDLRFLnrelrrlGGPPLPNPWIDTLRL--ARRLLPGLRSHRLGLLLAERYGIPLEGAHRALADALATAELL 158


                .
gi 19113423 243 K 243
Cdd:cd06127 159 L 159
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 119-251 1.10e-08

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 53.22  E-value: 1.10e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423 119 HGHVV--YDTYVRPKEKV----------TDwrtwvsgvksfHM-RDAPSFEKVQAEVAKILDNRVLVGHAVHNDLKVL-- 183
Cdd:COG2176  37 NGEIVdrFSTLVNPGRPIppfiteltgiTD-----------EMvADAPPFEEVLPEFLEFLGDAVLVAHNASFDLGFLna 105

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19113423 184 -----LLSHPRRMIrDTSRFSgyRKLAKG-RTPGLKKLAEViLGRDIqSGQHSSVQDAQATMELYKKVKKEMDE 251
Cdd:COG2176 106 alkrlGLPFDNPVL-DTLELA--RRLLPElKSYKLDTLAER-LGIPL-EDRHRALGDAEATAELFLKLLEKLEE 174
PRK07247 PRK07247
3'-5' exonuclease;
87-244 1.57e-06

3'-5' exonuclease;


Pssm-ID: 180906 [Multi-domain]  Cd Length: 195  Bit Score: 47.47  E-value: 1.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423   87 LETLGKYIAMDCEMVGVaDDMSVLARVSIVNYHGHV---VYDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVA 163
Cdd:PRK07247   1 MKRLETYIAFDLEFNTV-NGVSHIIQVSAVKYDDHKevdSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  164 KILDNRVLVGH-AVHNDLKVL------LLSHPRRMIRDTS---RFSGYRKLAKGRtpgLKKLAEvILGrdIQSGQHSSVQ 233
Cdd:PRK07247  80 EFVGELPLIGYnAQKSDLPILaengldLSDQYQVDLYDEAferRSSDLNGIANLK---LQTVAD-FLG--IKGRGHNSLE 153

                        170
                 ....*....|.
gi 19113423  234 DAQATMELYKK 244
Cdd:PRK07247 154 DARMTARVYES 164
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 120-183 7.41e-06

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: 44.81  E-value: 7.41e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19113423 120 GHVV--YDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKILDNRVLVGHAVHNDLKVL 183
Cdd:cd06130  27 GQIVdtFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLVVAHNASFDRSVL 92
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 88-249 3.19e-05

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 44.68  E-value: 3.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423   88 ETLGKYIAMDCEMVGvADDMSVLARVSIVNYHGHVVYDTY---VRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAK 164
Cdd:PRK07246   4 KKLRKYAVVDLEATG-AGPNASIIQVGIVIIEGGEIIDSYttdVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYD 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423  165 ILDNRVLVGHAVHNDLKVLL---------LSHPRrmiRDTSrfsgyrKLAKGRTPGLKK-----LAEViLGRDIqSGQHS 230
Cdd:PRK07246  83 LIEDCIFVAHNVKFDANLLAealflegyeLRTPR---VDTV------ELAQVFFPTLEKyslshLSRE-LNIDL-ADAHT 151

                        170
                 ....*....|....*....
gi 19113423  231 SVQDAQATMELYKKVKKEM 249
Cdd:PRK07246 152 AIADARATAELFLKLLQKI 170
PRK06807 PRK06807
3'-5' exonuclease;
93-183 1.99e-04

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 42.11  E-value: 1.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423   93 YIAMDCEMVGVADDMSVLARVSIVNYHGHVV---YDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKILDNR 169
Cdd:PRK06807  10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELvdqFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89

                         90
                 ....*....|....
gi 19113423  170 VLVGHAVHNDLKVL 183
Cdd:PRK06807  90 VIVAHNASFDMRFL 103
PRK06063 PRK06063
DEDDh family exonuclease;
139-176 3.07e-04

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 41.22  E-value: 3.07e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 19113423  139 TWVSGVKSFHMRDAPSFEKVQAEVAKILDNRVLVGHAV 176
Cdd:PRK06063  65 THVHGLTAEMLEGQPQFADIAGEVAELLRGRTLVAHNV 102
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 92-183 3.14e-04

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 41.86  E-value: 3.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423   92 KYIAMDCEMVGVA----DDMSVLARVSIVNyhGHVV--YDTYVRPKEKVTDWRTWVSGVKSFHMRDAPSFEKVQAEVAKI 165
Cdd:PRK08074   4 RFVVVDLETTGNSpkkgDKIIQIAAVVVED--GEILerFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVEL 81

                         90
                 ....*....|....*...
gi 19113423  166 LDNRVLVGHAVHNDLKVL 183
Cdd:PRK08074  82 LEGAYFVAHNVHFDLNFL 99
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 92-250 4.57e-03

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: 36.90  E-value: 4.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423    92 KYIAMDCEMVGV--ADDMSVLARVSIVNYHGHVVYDTYvrpkeKVTDWrtWVSGVKsfhmrdaPSFEKvqaevakilDNR 169
Cdd:pfam01612  21 PYVAVDTETTSLdtYSYYLRGALIQIGTGEGAYIIDPL-----ALGDD--VLSALK-------RLLED---------PNI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113423   170 VLVGHAVHNDLKVLLLSH---PRRMIrDTsRFSGYrKLAKGRTPGLKKLAEVILGRDIQSGQHSS--------------- 231
Cdd:pfam01612  78 TKVGHNAKFDLEVLARDFgikLRNLF-DT-MLAAY-LLGYDRSHSLADLAEKYLGVELDKEEQCSdwqarplseeqlrya 154

                         170
                  ....*....|....*....
gi 19113423   232 VQDAQATMELYKKVKKEMD 250
Cdd:pfam01612 155 ALDADYLLRLYDKLRKELE 173
 
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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