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Conserved domains on  [gi|1385123345|ref|NP_001349805|]
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RNA exonuclease 4 isoform 2 [Mus musculus]

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
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 ...
 254-379 4.82e-79

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: 240.50  E-value: 4.82e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPKGEESIAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRIL 333
Cdd:cd06144     1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1385123345 334 VGHALHNDLK-------------------------SGRPSLKRLSEKILGIRVQQAEHCSIQDAQAAMRLY 379
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 ...
 254-379 4.82e-79

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: 240.50  E-value: 4.82e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPKGEESIAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRIL 333
Cdd:cd06144     1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1385123345 334 VGHALHNDLK-------------------------SGRPSLKRLSEKILGIRVQQAEHCSIQDAQAAMRLY 379
Cdd:cd06144    81 VGHALKNDLKvlkldhpkklirdtskykplrktakGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 254-387 1.84e-33

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 122.79  E-value: 1.84e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345  254 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGR 331
Cdd:smart00479   3 VVIDCETTGLDPGKDEiiEIAA-VDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345  332 ILV-GHALHNDLK--------------------------------SGRPSLKRLSEKiLGIRVQQAEHCSIQDAQAAMRL 378
Cdd:smart00479  82 ILVaGNSAHFDLRflklehprlgikqppklpvidtlklaratnpgLPKYSLKKLAKR-LLLEVIQRAHRALDDARATAKL 160


                   ....*....
gi 1385123345  379 YVMVKREWE 387
Cdd:smart00479 161 FKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 254-379 8.89e-19

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: 82.78  E-value: 8.89e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPKGEESIA-ARVSIVN--QYGKCVYDKYVKPTEP--VTDYRTAVSGIRPENLKQGEEFEVVKKEVAEML 328
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEiAAVVIDGgeNEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 329 KG---------RILVGHALHNDLKSG-------------------------RPSLKRLSEKiLGIRVQQAEHCSIQDAQA 374
Cdd:pfam00929  81 RKgnllvahnaSFDVGFLRYDDKRFLkkpmpklnpvidtlildkatykelpGRSLDALAEK-LGLEHIGRAHRALDDARA 159


                  ....*
gi 1385123345 375 AMRLY 379
Cdd:pfam00929 160 TAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 254-343 5.15e-12

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 63.66  E-value: 5.15e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGR 331
Cdd:COG0847     3 VVLDTETTGLDPAKDRiiEIGA-VKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81

                          90
                  ....*....|..
gi 1385123345 332 ILVGHALHNDLK 343
Cdd:COG0847    82 VLVAHNAAFDLG 93
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 257-342 2.39e-04

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 43.40  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 257 DCEMVGVGPKGEESIAARVSIVNQYGKCV--YDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRILV 334
Cdd:PRK08074    9 DLETTGNSPKKGDKIIQIAAVVVEDGEILerFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEGAYFV 88


                  ....*...
gi 1385123345 335 GHALHNDL 342
Cdd:PRK08074   89 AHNVHFDL 96
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 289-356 8.87e-04

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: 40.51  E-value: 8.87e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1385123345 289 YVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRILVGHALHNDLKSGRPSLKRLSEKI 356
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVE 113
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 254-379 4.82e-79

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: 240.50  E-value: 4.82e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPKGEESIAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRIL 333
Cdd:cd06144     1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1385123345 334 VGHALHNDLK-------------------------SGRPSLKRLSEKILGIRVQQAEHCSIQDAQAAMRLY 379
Cdd:cd06144    81 VGHALKNDLKvlkldhpkklirdtskykplrktakGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 254-379 3.78e-46

DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.


Pssm-ID: 99852  Cd Length: 157  Bit Score: 156.06  E-value: 3.78e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPKGEESIAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRIL 333
Cdd:cd06149     1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1385123345 334 VGHALHNDLKS----------------------------GRPSLKRLSEKIL--GIRVQQAEHCSIQDAQAAMRLY 379
Cdd:cd06149    81 VGHAIHNDFKAlkyfhpkhmtrdtstipllnrkagfpenCRVSLKVLAKRLLhrDIQVGRQGHSSVEDARATMELY 156
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 254-378 5.13e-38

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: 134.54  E-value: 5.13e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGpKGEEsiAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQ-GEEFEVVKKEVAEML-KGR 331
Cdd:cd06145     1 FALDCEMCYTT-DGLE--LTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENvTTTLEDVQKKLLSLIsPDT 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1385123345 332 ILVGHALHNDLKS----------------------GRPSLKRLSEKILGIRVQQ--AEHCSIQDAQAAMRL 378
Cdd:cd06145    78 ILVGHSLENDLKAlklihprvidtailfphprgppYKPSLKNLAKKYLGRDIQQgeGGHDSVEDARAALEL 148
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 254-387 1.84e-33

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 122.79  E-value: 1.84e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345  254 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGR 331
Cdd:smart00479   3 VVIDCETTGLDPGKDEiiEIAA-VDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345  332 ILV-GHALHNDLK--------------------------------SGRPSLKRLSEKiLGIRVQQAEHCSIQDAQAAMRL 378
Cdd:smart00479  82 ILVaGNSAHFDLRflklehprlgikqppklpvidtlklaratnpgLPKYSLKKLAKR-LLLEVIQRAHRALDDARATAKL 160


                   ....*....
gi 1385123345  379 YVMVKREWE 387
Cdd:smart00479 161 FKKLLERLE 169
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 255-379 1.72e-24

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.


Pssm-ID: 99840  Cd Length: 161  Bit Score: 98.51  E-value: 1.72e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 255 ALDCEMVGVGPKGEESIaaRVSIVNQY-GKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEE-------FEVVKKEVAE 326
Cdd:cd06137     2 ALDCEMVGLADGDSEVV--RISAVDVLtGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKagktifgWEAARAALWK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 327 MLKGR-ILVGHALHNDLKS-------------------GRP------SLKRLSEKILGIRVQQAE--HCSIQDAQAAMRL 378
Cdd:cd06137    80 FIDPDtILVGHSLQNDLDAlrmihtrvvdtailtreavKGPlakrqwSLRTLCRDFLGLKIQGGGegHDSLEDALAAREV 159


                  .
gi 1385123345 379 Y 379
Cdd:cd06137   160 V 160
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 254-379 8.89e-19

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: 82.78  E-value: 8.89e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPKGEESIA-ARVSIVN--QYGKCVYDKYVKPTEP--VTDYRTAVSGIRPENLKQGEEFEVVKKEVAEML 328
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEiAAVVIDGgeNEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 329 KG---------RILVGHALHNDLKSG-------------------------RPSLKRLSEKiLGIRVQQAEHCSIQDAQA 374
Cdd:pfam00929  81 RKgnllvahnaSFDVGFLRYDDKRFLkkpmpklnpvidtlildkatykelpGRSLDALAEK-LGLEHIGRAHRALDDARA 159


                  ....*
gi 1385123345 375 AMRLY 379
Cdd:pfam00929 160 TAKLF 164
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 254-379 9.28e-19

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: 83.05  E-value: 9.28e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPK-------GEESI-------AARVSIV----NQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENL--KQ 313
Cdd:cd06143     1 VAIDAEFVKLKPEeteirsdGTKSTirpsqmsLARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLdpKT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 314 GEEFEVVKKEVAEMLK-----GRILVGHALHNDLK----------------------SGRPSLKRLSEKILGIRVQQAEH 366
Cdd:cd06143    81 SSKNLTTLKSAYLKLRllvdlGCIFVGHGLAKDFRviniqvpkeqvidtvelfhlpgQRKLSLRFLAWYLLGEKIQSETH 160

                         170
                  ....*....|...
gi 1385123345 367 CSIQDAQAAMRLY 379
Cdd:cd06143   161 DSIEDARTALKLY 173
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 254-379 8.18e-14

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: 68.87  E-value: 8.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCV-YDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKG 330
Cdd:cd06127     1 VVFDTETTGLDPKKDRiiEIGA-VKVDGGIEIVErFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 331 RILVGH---------------------------------ALHNDLKSGRpsLKRLSEKILGIRVQQAeHCSIQDAQAAMR 377
Cdd:cd06127    80 RVLVAHnasfdlrflnrelrrlggpplpnpwidtlrlarRLLPGLRSHR--LGLLLAERYGIPLEGA-HRALADALATAE 156


                  ..
gi 1385123345 378 LY 379
Cdd:cd06127   157 LL 158
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 254-343 5.15e-12

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 63.66  E-value: 5.15e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 254 LALDCEMVGVGPKGEE--SIAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGR 331
Cdd:COG0847     3 VVLDTETTGLDPAKDRiiEIGA-VKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81

                          90
                  ....*....|..
gi 1385123345 332 ILVGHALHNDLK 343
Cdd:COG0847    82 VLVAHNAAFDLG 93
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 257-342 2.39e-04

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 43.40  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 257 DCEMVGVGPKGEESIAARVSIVNQYGKCV--YDKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRILV 334
Cdd:PRK08074    9 DLETTGNSPKKGDKIIQIAAVVVEDGEILerFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEGAYFV 88


                  ....*...
gi 1385123345 335 GHALHNDL 342
Cdd:PRK08074   89 AHNVHFDL 96
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 289-356 8.87e-04

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: 40.51  E-value: 8.87e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1385123345 289 YVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRILVGHALHNDLKSGRPSLKRLSEKI 356
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVE 113
PRK09145 PRK09145
3'-5' exonuclease;
229-363 2.50e-03

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 38.73  E-value: 2.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1385123345 229 RKRLGQKKRTisleKEQAFGGL------TKALALDCEMVGVGPKGEE--SIAArVSIVNqyGKCVYDK----YVKPTEPV 296
Cdd:PRK09145    5 LRRLWWRRRL----KDPRYAFLfeppppDEWVALDCETTGLDPRRAEivSIAA-VKIRG--NRILTSErlelLVRPPQSL 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1385123345 297 TDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRILVGHALHNDLKSGRPSLKRLsekiLGIRVQQ 363
Cdd:PRK09145   78 SAESIKIHRLRHQDLEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPL----LGIPLPN 140
 
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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