NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|76563954|ref|NP_001029056|]
View 

RNA exonuclease 4 [Rattus norvegicus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 231-381 6.29e-98

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: 288.65  E-value: 6.29e-98
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 231 LALDCEMVGVGPKGEESIAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGRIL 310
Cdd:cd06144   1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 76563954 311 VGHALRNDLKVLFLEHPKKKIRDTQKFKPFRSLVKSARPSLKQLSEKILGLRVQQAEHCSVQDAQAAMRLY 381
Cdd:cd06144  81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 231-381 6.29e-98

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: 288.65  E-value: 6.29e-98
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 231 LALDCEMVGVGPKGEESIAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGRIL 310
Cdd:cd06144   1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 76563954 311 VGHALRNDLKVLFLEHPKKKIRDTQKFKPFRSLVKSARPSLKQLSEKILGLRVQQAEHCSVQDAQAAMRLY 381
Cdd:cd06144  81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 231-389 3.66e-42

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 145.91  E-value: 3.66e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954    231 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGR 308
Cdd:smart00479   3 VVIDCETTGLDPGKDEiiEIAA-VDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954    309 ILV-GHALRNDLKVLFLEHPKKK--------IRDTQKFKPFRSLVKSaRPSLKQLSEKiLGLRVQQAEHCSVQDAQAAMR 379
Cdd:smart00479  82 ILVaGNSAHFDLRFLKLEHPRLGikqppklpVIDTLKLARATNPGLP-KYSLKKLAKR-LLLEVIQRAHRALDDARATAK 159

                          170
                   ....*....|
gi 76563954    380 LYIMVKRKWE 389
Cdd:smart00479 160 LFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 231-381 1.74e-23

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: 95.88  E-value: 1.74e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954   231 LALDCEMVGVGPKGEESIA-ARVSIVN--QYGKCVYDKYVKPTEP--VTDYRTAVSGIRPENLKQGEEFEVVKKEVAAML 305
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEiAAVVIDGgeNEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954   306 KG---------RILVGHALRNDLKVLFLEHPKK-KIRDTQKFkpFRSLVKS-ARPSLKQLSEKiLGLRVQQAEHCSVQDA 374
Cdd:pfam00929  81 RKgnllvahnaSFDVGFLRYDDKRFLKKPMPKLnPVIDTLIL--DKATYKElPGRSLDALAEK-LGLEHIGRAHRALDDA 157


                  ....*..
gi 76563954   375 QAAMRLY 381
Cdd:pfam00929 158 RATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 231-382 3.70e-16

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 75.60  E-value: 3.70e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 231 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGR 308
Cdd:COG0847   3 VVLDTETTGLDPAKDRiiEIGA-VKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 309 ILVGHALRNDLKVL-------FLEHPKKKIRDTQKFkpFRSLVKSARP-SLKQLSEKiLGLRVQQAeHCSVQDAQAAMRL 380
Cdd:COG0847  82 VLVAHNAAFDLGFLnaelrraGLPLPPFPVLDTLRL--ARRLLPGLPSySLDALCER-LGIPFDER-HRALADAEATAEL 157


                ..
gi 76563954 381 YI 382
Cdd:COG0847 158 FL 159
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 266-393 2.07e-05

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: 45.52  E-value: 2.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954   266 YVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGRILVGHALRNDLKVLFLEHPK--KKIRDTQKFKPFRSL 343
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKlyKVEPKTNDVIDTTDT 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 76563954   344 VKSARPSL--KQLSEKILGLRV-----QQAEHCSVQDAQAAMRLYIMVKRKWESIAA 393
Cdd:TIGR00573 126 LQYARPEFpgKRNTLDALCKRYeitnsHRALHGALADAFILAKLYLVMTGKQTKYGE 182
PRK09145 PRK09145
3'-5' exonuclease;
232-322 7.18e-04

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 40.66  E-value: 7.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954  232 ALDCEMVGVGPKGEE--SIAArVSIVNqyGKCVYDK----YVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAML 305
Cdd:PRK09145  33 ALDCETTGLDPRRAEivSIAA-VKIRG--NRILTSErlelLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFI 109

                         90
                 ....*....|....*..
gi 76563954  306 KGRILVGHALRNDLKVL 322
Cdd:PRK09145 110 GNRPLVGYYLEFDVAML 126
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 231-381 6.29e-98

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: 288.65  E-value: 6.29e-98
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 231 LALDCEMVGVGPKGEESIAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGRIL 310
Cdd:cd06144   1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 76563954 311 VGHALRNDLKVLFLEHPKKKIRDTQKFKPFRSLVKSARPSLKQLSEKILGLRVQQAEHCSVQDAQAAMRLY 381
Cdd:cd06144  81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 231-381 4.00e-55

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: 179.17  E-value: 4.00e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 231 LALDCEMVGVGPKGEESIAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGRIL 310
Cdd:cd06149   1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 76563954 311 VGHALRNDLKVLFLEHPKKKIRDTQKFKPFRSLVK---SARPSLKQLSEKILGLRVQQAE--HCSVQDAQAAMRLY 381
Cdd:cd06149  81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGfpeNCRVSLKVLAKRLLHRDIQVGRqgHSSVEDARATMELY 156
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 231-389 3.66e-42

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 145.91  E-value: 3.66e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954    231 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGR 308
Cdd:smart00479   3 VVIDCETTGLDPGKDEiiEIAA-VDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954    309 ILV-GHALRNDLKVLFLEHPKKK--------IRDTQKFKPFRSLVKSaRPSLKQLSEKiLGLRVQQAEHCSVQDAQAAMR 379
Cdd:smart00479  82 ILVaGNSAHFDLRFLKLEHPRLGikqppklpVIDTLKLARATNPGLP-KYSLKKLAKR-LLLEVIQRAHRALDDARATAK 159

                          170
                   ....*....|
gi 76563954    380 LYIMVKRKWE 389
Cdd:smart00479 160 LFKKLLERLE 169
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 231-380 3.06e-41

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: 143.01  E-value: 3.06e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 231 LALDCEMVGVGpKGEEsiAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQ-GEEFEVVKKEVAAML-KGR 308
Cdd:cd06145   1 FALDCEMCYTT-DGLE--LTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENvTTTLEDVQKKLLSLIsPDT 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 309 ILVGHALRNDLKVLFLEHPkkKIRDT------QKFKPFrslvksaRPSLKQLSEKILGLRVQQ--AEHCSVQDAQAAMRL 380
Cdd:cd06145  78 ILVGHSLENDLKALKLIHP--RVIDTailfphPRGPPY-------KPSLKNLAKKYLGRDIQQgeGGHDSVEDARAALEL 148
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 232-381 1.50e-28

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: 109.68  E-value: 1.50e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 232 ALDCEMVGVGPKGEESIaaRVSIVNQY-GKCVYDKYVKPTEPVTDYRTAVSGIRPENL----KQGEefEVVKKEVAAMLK 306
Cdd:cd06137   2 ALDCEMVGLADGDSEVV--RISAVDVLtGEVLIDSLVRPSVRVTDWRTRFSGVTPADLeeaaKAGK--TIFGWEAARAAL 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 307 GR------ILVGHALRNDLKVLFLEHPkkKIRDTQKFkpFRSLVKSARP----SLKQLSEKILGLRVQQAE--HCSVQDA 374
Cdd:cd06137  78 WKfidpdtILVGHSLQNDLDALRMIHT--RVVDTAIL--TREAVKGPLAkrqwSLRTLCRDFLGLKIQGGGegHDSLEDA 153


                ....*..
gi 76563954 375 QAAMRLY 381
Cdd:cd06137 154 LAAREVV 160
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 231-381 3.03e-25

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: 101.15  E-value: 3.03e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 231 LALDCEMVGVGPK-------GEESI-------AARVSIV----NQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENL--KQ 290
Cdd:cd06143   1 VAIDAEFVKLKPEeteirsdGTKSTirpsqmsLARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLdpKT 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 291 GEEFEVVKKevAAMLK-------GRILVGHALRNDLKVLFLEHPKKKIRDTQK--FKP-FRSLvksarpSLKQLSEKILG 360
Cdd:cd06143  81 SSKNLTTLK--SAYLKlrllvdlGCIFVGHGLAKDFRVINIQVPKEQVIDTVElfHLPgQRKL------SLRFLAWYLLG 152

                       170       180
                ....*....|....*....|.
gi 76563954 361 LRVQQAEHCSVQDAQAAMRLY 381
Cdd:cd06143 153 EKIQSETHDSIEDARTALKLY 173
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 231-381 1.74e-23

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: 95.88  E-value: 1.74e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954   231 LALDCEMVGVGPKGEESIA-ARVSIVN--QYGKCVYDKYVKPTEP--VTDYRTAVSGIRPENLKQGEEFEVVKKEVAAML 305
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEiAAVVIDGgeNEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954   306 KG---------RILVGHALRNDLKVLFLEHPKK-KIRDTQKFkpFRSLVKS-ARPSLKQLSEKiLGLRVQQAEHCSVQDA 374
Cdd:pfam00929  81 RKgnllvahnaSFDVGFLRYDDKRFLKKPMPKLnPVIDTLIL--DKATYKElPGRSLDALAEK-LGLEHIGRAHRALDDA 157


                  ....*..
gi 76563954   375 QAAMRLY 381
Cdd:pfam00929 158 RATAKLF 164
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 231-382 1.04e-18

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: 82.35  E-value: 1.04e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 231 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCV-YDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKG 307
Cdd:cd06127   1 VVFDTETTGLDPKKDRiiEIGA-VKVDGGIEIVErFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 308 RILVGHALRNDLKVL-------FLEHPKKKIRDTQKFkpFRSLVKSARP-SLKQLSEKILGLRVQQAeHCSVQDAQAAMR 379
Cdd:cd06127  80 RVLVAHNASFDLRFLnrelrrlGGPPLPNPWIDTLRL--ARRLLPGLRShRLGLLLAERYGIPLEGA-HRALADALATAE 156


                ...
gi 76563954 380 LYI 382
Cdd:cd06127 157 LLL 159
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 231-382 3.70e-16

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 75.60  E-value: 3.70e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 231 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGR 308
Cdd:COG0847   3 VVLDTETTGLDPAKDRiiEIGA-VKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 309 ILVGHALRNDLKVL-------FLEHPKKKIRDTQKFkpFRSLVKSARP-SLKQLSEKiLGLRVQQAeHCSVQDAQAAMRL 380
Cdd:COG0847  82 VLVAHNAAFDLGFLnaelrraGLPLPPFPVLDTLRL--ARRLLPGLPSySLDALCER-LGIPFDER-HRALADAEATAEL 157


                ..
gi 76563954 381 YI 382
Cdd:COG0847 158 FL 159
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 266-393 2.07e-05

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: 45.52  E-value: 2.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954   266 YVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGRILVGHALRNDLKVLFLEHPK--KKIRDTQKFKPFRSL 343
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKlyKVEPKTNDVIDTTDT 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 76563954   344 VKSARPSL--KQLSEKILGLRV-----QQAEHCSVQDAQAAMRLYIMVKRKWESIAA 393
Cdd:TIGR00573 126 LQYARPEFpgKRNTLDALCKRYeitnsHRALHGALADAFILAKLYLVMTGKQTKYGE 182
PRK09145 PRK09145
3'-5' exonuclease;
232-322 7.18e-04

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 40.66  E-value: 7.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954  232 ALDCEMVGVGPKGEE--SIAArVSIVNqyGKCVYDK----YVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAML 305
Cdd:PRK09145  33 ALDCETTGLDPRRAEivSIAA-VKIRG--NRILTSErlelLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFI 109

                         90
                 ....*....|....*..
gi 76563954  306 KGRILVGHALRNDLKVL 322
Cdd:PRK09145 110 GNRPLVGYYLEFDVAML 126
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 263-382 8.95e-04

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: 39.90  E-value: 8.95e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954 263 YDKYVKPTE--PVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGRILVGHAL--RNDLKVLFLEHPKKKIRDTQKFK 338
Cdd:cd06133  42 FSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFVTwgDWDLKDLLQNQCKYKIINLPPFF 121

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 76563954 339 P---------FRSLVKSARPSLKQLSEkILGLRVQQAEHCSVQDAQAAMRLYI 382
Cdd:cd06133 122 RqwidlkkefAKFYGLKKRTGLSKALE-YLGLEFEGRHHRGLDDARNIARILK 173
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 234-326 2.18e-03

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 40.32  E-value: 2.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76563954  234 DCEMVGVGPKGEESIAARVSIVNQYGKCV--YDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAAMLKGRILV 311
Cdd:PRK08074   9 DLETTGNSPKKGDKIIQIAAVVVEDGEILerFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEGAYFV 88

                         90
                 ....*....|....*
gi 76563954  312 GHALRNDLKvlFLEH 326
Cdd:PRK08074  89 AHNVHFDLN--FLNE 101
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH