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Conserved domains on  [gi|1679885188]
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Chain A, PAN2-PAN3 deadenylation complex catalytic subunit PAN2

Protein Classification

PAN2-PAN3 deadenylation complex catalytic subunit PAN2( domain architecture ID 12138561)

PAN2-PAN3 deadenylation complex catalytic subunit PAN2 is the catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
464-637 1.04e-100

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: 305.31  E-value: 1.04e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 464 VAIDAAFVSLQSELCEIDHQGIRSIIRPKRTALARISIIRGEeGELYGVPFVDDYVVNTNHIEDYLTRYSGILPGDLDPE 543
Cdd:cd06143     1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGE-GELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 544 KSTKRLVRRNVVYRKVWLLMQLGCVFVGHGLNNDFKHININVPRNQIRDTA-IYFLQGKRYLSLRYLAYVLLGMNIQEGN 622
Cdd:cd06143    80 TSSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVeLFHLPGQRKLSLRFLAWYLLGEKIQSET 159
                         170
                  ....*....|....*
gi 1679885188 623 HDSIEDAHTALILYK 637
Cdd:cd06143   160 HDSIEDARTALKLYR 174
UCH_1 pfam13423
Ubiquitin carboxyl-terminal hydrolase;
62-386 2.40e-64

Ubiquitin carboxyl-terminal hydrolase;


:

Pssm-ID: 463872 [Multi-domain]  Cd Length: 305  Bit Score: 215.21  E-value: 2.40e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188  62 SGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENF-ETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTDKRQL 140
Cdd:pfam13423   1 SGLETHIPNSYTNSLLQLLRFIPPLRNLALSHLATECLkEHCLLCELGFLFDMLEKAKGKNCQASNFLRALSSIPEASAL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 141 EngepqehleeyleslcIRESIEDFNSSESIkRNMPQKFNRFLLSQLIKEEAQTVNHNI----TLNQCFG--LETEIRTe 214
Cdd:pfam13423  81 G----------------LLDEDRETNSAISL-SSLIQSFNRFLLDQLSSEENSTPPNPSpaesPLEQLFGidAETTIRC- 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 215 CSCDHYdtTVKLLPSLSISGINKTVIKQLNKKSNGQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSL 294
Cdd:pfam13423 143 SNCGHE--SVRESSTHVLDLIYPRKPSSNNKKPPNQTFSSILKSSLERETTTKAWCEKCKRYQPLESRRTVRNLPPVLSL 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 295 ELSLLDTEFSNIRSSKNWLTSEFYGSIiknkavlrstASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVK---KYNP 371
Cdd:pfam13423 221 NAALTNEEWRQLWKTPGWLPPEIGLTL----------SDDLQGDNEIVKYELRGVVVHIGDSGTSGHLVSFVKvadSELE 290
                         330
                  ....*....|....*
gi 1679885188 372 KENCFKWLMFNDYLV 386
Cdd:pfam13423 291 DPTESQWYLFNDFLV 305
 
Name Accession Description Interval E-value
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
464-637 1.04e-100

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: 305.31  E-value: 1.04e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 464 VAIDAAFVSLQSELCEIDHQGIRSIIRPKRTALARISIIRGEeGELYGVPFVDDYVVNTNHIEDYLTRYSGILPGDLDPE 543
Cdd:cd06143     1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGE-GELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 544 KSTKRLVRRNVVYRKVWLLMQLGCVFVGHGLNNDFKHININVPRNQIRDTA-IYFLQGKRYLSLRYLAYVLLGMNIQEGN 622
Cdd:cd06143    80 TSSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVeLFHLPGQRKLSLRFLAWYLLGEKIQSET 159
                         170
                  ....*....|....*
gi 1679885188 623 HDSIEDAHTALILYK 637
Cdd:cd06143   160 HDSIEDARTALKLYR 174
UCH_1 pfam13423
Ubiquitin carboxyl-terminal hydrolase;
62-386 2.40e-64

Ubiquitin carboxyl-terminal hydrolase;


Pssm-ID: 463872 [Multi-domain]  Cd Length: 305  Bit Score: 215.21  E-value: 2.40e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188  62 SGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENF-ETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTDKRQL 140
Cdd:pfam13423   1 SGLETHIPNSYTNSLLQLLRFIPPLRNLALSHLATECLkEHCLLCELGFLFDMLEKAKGKNCQASNFLRALSSIPEASAL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 141 EngepqehleeyleslcIRESIEDFNSSESIkRNMPQKFNRFLLSQLIKEEAQTVNHNI----TLNQCFG--LETEIRTe 214
Cdd:pfam13423  81 G----------------LLDEDRETNSAISL-SSLIQSFNRFLLDQLSSEENSTPPNPSpaesPLEQLFGidAETTIRC- 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 215 CSCDHYdtTVKLLPSLSISGINKTVIKQLNKKSNGQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSL 294
Cdd:pfam13423 143 SNCGHE--SVRESSTHVLDLIYPRKPSSNNKKPPNQTFSSILKSSLERETTTKAWCEKCKRYQPLESRRTVRNLPPVLSL 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 295 ELSLLDTEFSNIRSSKNWLTSEFYGSIiknkavlrstASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVK---KYNP 371
Cdd:pfam13423 221 NAALTNEEWRQLWKTPGWLPPEIGLTL----------SDDLQGDNEIVKYELRGVVVHIGDSGTSGHLVSFVKvadSELE 290
                         330
                  ....*....|....*
gi 1679885188 372 KENCFKWLMFNDYLV 386
Cdd:pfam13423 291 DPTESQWYLFNDFLV 305
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
462-644 1.12e-27

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 109.70  E-value: 1.12e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188  462 TLVAIDAAFVSLQselceidhqgirsiirPKRTALARISIIRGEEGELygVPFVDDYVVNTNHIEDYLTRYSGILPGDLD 541
Cdd:smart00479   1 TLVVIDCETTGLD----------------PGKDEIIEIAAVDVDGGEI--IEVFDTYVKPDRPITDYATEIHGITPEMLD 62
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188  542 PEKSTKrlvrrnVVYRKVWLLMQLGCVFVGHGLNNDFKHININVPR--------NQIRDTAIY---FLQGKRYLSLRYLA 610
Cdd:smart00479  63 DAPTFE------EVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRlgikqppkLPVIDTLKLaraTNPGLPKYSLKKLA 136
                          170       180       190
                   ....*....|....*....|....*....|....
gi 1679885188  611 YVLLGMNIQEGnHDSIEDAHTALILYKKYLHLKE 644
Cdd:smart00479 137 KRLLLEVIQRA-HRALDDARATAKLFKKLLERLE 169
Peptidase_C19P cd02672
A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are ...
47-391 3.98e-25

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.


Pssm-ID: 239137 [Multi-domain]  Cd Length: 268  Bit Score: 105.29  E-value: 3.98e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188  47 GTDNFDFTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENFETTLLTDLGYLFDMMersHGKICsssn 126
Cdd:cd02672     1 GTEDFDFEFYNKTNYAGLENHITNSYCNSLLQLLYFIPPFRNFTAIILVACPKESCLLCELGYLFSTL---IQNFT---- 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 127 fqaslksltdkRQLENGEPQEHLEEYLESLCIRESIedfnssesikrnmpqkfnrFLLSQL-IKEEAQTVNHNITLNQCF 205
Cdd:cd02672    74 -----------RFLLETISQDQLGTPFSCGTSRNSV-------------------SLLYTLsLPLGSTKTSKESTFLQLL 123
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 206 --GLETEIRTECSCD--------HYDTTVKLLPSLSISGINKTVIKQLNKKSNGQNILPYIEYAMKNVTQKNSICPTCGK 275
Cdd:cd02672   124 krSLDLEKVTKAWCDtcckyqplEQTTSIRHLPDILLLVLVINLSVTNGEFDDINVVLPSGKVMQNKVSPKAIDHDKLVK 203
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 276 TETITQectvknlpsvlslelslldtefsnirssknwltsefygsiiknkavlrstaselkgtshIFKYELNGYVAKITD 355
Cdd:cd02672   204 NRGQES-----------------------------------------------------------IYKYELVGYVCEIND 224
                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1679885188 356 NNNETRLVTYVKKYNPKENCFKWLMFNDYLVVEITE 391
Cdd:cd02672   225 SSRGQHNVVFVIKVNEESTHGRWYLFNDFLVTPVSE 260
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
464-636 8.79e-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: 95.50  E-value: 8.79e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 464 VAIDAAFVSLQselceidhqgirsIIRPKRTALARISIIRGEEGElygVPFVDDYVVNT--NHIEDYLTRYSGILPGDLD 541
Cdd:pfam00929   1 VVIDLETTGLD-------------PEKDEIIEIAAVVIDGGENEI---GETFHTYVKPTrlPKLTDECTKFTGITQAMLD 64
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 542 PEKSTK-RLVRRNVVYRKVWLLMQLG-CVFVGHGLNNDFKHININVP-RNQIRDTAIYF---LQGKRYLSLRYLAYVLLG 615
Cdd:pfam00929  65 NKPSFEeVLEEFLEFLRKGNLLVAHNaSFDVGFLRYDDKRFLKKPMPkLNPVIDTLILDkatYKELPGRSLDALAEKLGL 144
                         170       180
                  ....*....|....*....|.
gi 1679885188 616 MNIQEgNHDSIEDAHTALILY 636
Cdd:pfam00929 145 EHIGR-AHRALDDARATAKLF 164
 
Name Accession Description Interval E-value
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
464-637 1.04e-100

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: 305.31  E-value: 1.04e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 464 VAIDAAFVSLQSELCEIDHQGIRSIIRPKRTALARISIIRGEeGELYGVPFVDDYVVNTNHIEDYLTRYSGILPGDLDPE 543
Cdd:cd06143     1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGE-GELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 544 KSTKRLVRRNVVYRKVWLLMQLGCVFVGHGLNNDFKHININVPRNQIRDTA-IYFLQGKRYLSLRYLAYVLLGMNIQEGN 622
Cdd:cd06143    80 TSSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVeLFHLPGQRKLSLRFLAWYLLGEKIQSET 159
                         170
                  ....*....|....*
gi 1679885188 623 HDSIEDAHTALILYK 637
Cdd:cd06143   160 HDSIEDARTALKLYR 174
UCH_1 pfam13423
Ubiquitin carboxyl-terminal hydrolase;
62-386 2.40e-64

Ubiquitin carboxyl-terminal hydrolase;


Pssm-ID: 463872 [Multi-domain]  Cd Length: 305  Bit Score: 215.21  E-value: 2.40e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188  62 SGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENF-ETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTDKRQL 140
Cdd:pfam13423   1 SGLETHIPNSYTNSLLQLLRFIPPLRNLALSHLATECLkEHCLLCELGFLFDMLEKAKGKNCQASNFLRALSSIPEASAL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 141 EngepqehleeyleslcIRESIEDFNSSESIkRNMPQKFNRFLLSQLIKEEAQTVNHNI----TLNQCFG--LETEIRTe 214
Cdd:pfam13423  81 G----------------LLDEDRETNSAISL-SSLIQSFNRFLLDQLSSEENSTPPNPSpaesPLEQLFGidAETTIRC- 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 215 CSCDHYdtTVKLLPSLSISGINKTVIKQLNKKSNGQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSL 294
Cdd:pfam13423 143 SNCGHE--SVRESSTHVLDLIYPRKPSSNNKKPPNQTFSSILKSSLERETTTKAWCEKCKRYQPLESRRTVRNLPPVLSL 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 295 ELSLLDTEFSNIRSSKNWLTSEFYGSIiknkavlrstASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVK---KYNP 371
Cdd:pfam13423 221 NAALTNEEWRQLWKTPGWLPPEIGLTL----------SDDLQGDNEIVKYELRGVVVHIGDSGTSGHLVSFVKvadSELE 290
                         330
                  ....*....|....*
gi 1679885188 372 KENCFKWLMFNDYLV 386
Cdd:pfam13423 291 DPTESQWYLFNDFLV 305
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
464-637 3.14e-29

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: 113.38  E-value: 3.14e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 464 VAIDAAFVslqselceidhqGIRSiiRPKRTALARISIIrGEEGE-LYgvpfvDDYVVNTNHIEDYLTRYSGILPGDLDP 542
Cdd:cd06144     1 VALDCEMV------------GVGP--DGSESALARVSIV-NEDGNvVY-----DTYVKPQEPVTDYRTAVSGIRPEHLKD 60
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 543 EKStkrlvrRNVVYRKVwllMQL--GCVFVGHGLNNDFKHININVPRNQIRDTAIY--FLQ--GKRYLSLRYLAYVLLGM 616
Cdd:cd06144    61 APD------FEEVQKKV---AELlkGRILVGHALKNDLKVLKLDHPKKLIRDTSKYkpLRKtaKGKSPSLKKLAKQLLGL 131
                         170       180
                  ....*....|....*....|.
gi 1679885188 617 NIQEGNHDSIEDAHTALILYK 637
Cdd:cd06144   132 DIQEGEHSSVEDARAAMRLYR 152
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
462-644 1.12e-27

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 109.70  E-value: 1.12e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188  462 TLVAIDAAFVSLQselceidhqgirsiirPKRTALARISIIRGEEGELygVPFVDDYVVNTNHIEDYLTRYSGILPGDLD 541
Cdd:smart00479   1 TLVVIDCETTGLD----------------PGKDEIIEIAAVDVDGGEI--IEVFDTYVKPDRPITDYATEIHGITPEMLD 62
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188  542 PEKSTKrlvrrnVVYRKVWLLMQLGCVFVGHGLNNDFKHININVPR--------NQIRDTAIY---FLQGKRYLSLRYLA 610
Cdd:smart00479  63 DAPTFE------EVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRlgikqppkLPVIDTLKLaraTNPGLPKYSLKKLA 136
                          170       180       190
                   ....*....|....*....|....*....|....
gi 1679885188  611 YVLLGMNIQEGnHDSIEDAHTALILYKKYLHLKE 644
Cdd:smart00479 137 KRLLLEVIQRA-HRALDDARATAKLFKKLLERLE 169
Peptidase_C19P cd02672
A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are ...
47-391 3.98e-25

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.


Pssm-ID: 239137 [Multi-domain]  Cd Length: 268  Bit Score: 105.29  E-value: 3.98e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188  47 GTDNFDFTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENFETTLLTDLGYLFDMMersHGKICsssn 126
Cdd:cd02672     1 GTEDFDFEFYNKTNYAGLENHITNSYCNSLLQLLYFIPPFRNFTAIILVACPKESCLLCELGYLFSTL---IQNFT---- 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 127 fqaslksltdkRQLENGEPQEHLEEYLESLCIRESIedfnssesikrnmpqkfnrFLLSQL-IKEEAQTVNHNITLNQCF 205
Cdd:cd02672    74 -----------RFLLETISQDQLGTPFSCGTSRNSV-------------------SLLYTLsLPLGSTKTSKESTFLQLL 123
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 206 --GLETEIRTECSCD--------HYDTTVKLLPSLSISGINKTVIKQLNKKSNGQNILPYIEYAMKNVTQKNSICPTCGK 275
Cdd:cd02672   124 krSLDLEKVTKAWCDtcckyqplEQTTSIRHLPDILLLVLVINLSVTNGEFDDINVVLPSGKVMQNKVSPKAIDHDKLVK 203
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 276 TETITQectvknlpsvlslelslldtefsnirssknwltsefygsiiknkavlrstaselkgtshIFKYELNGYVAKITD 355
Cdd:cd02672   204 NRGQES-----------------------------------------------------------IYKYELVGYVCEIND 224
                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1679885188 356 NNNETRLVTYVKKYNPKENCFKWLMFNDYLVVEITE 391
Cdd:cd02672   225 SSRGQHNVVFVIKVNEESTHGRWYLFNDFLVTPVSE 260
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
464-636 1.85e-23

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: 97.35  E-value: 1.85e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 464 VAIDAAFVSLQSELCEidhqgirsiirpkrtaLARISIIRGEEGElygvPFVDDYVVNTNHIEDYLTRYSGILPGDLDPE 543
Cdd:cd06137     1 VALDCEMVGLADGDSE----------------VVRISAVDVLTGE----VLIDSLVRPSVRVTDWRTRFSGVTPADLEEA 60
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 544 KSTKRLVRRNVVYRK-VWLLMQLGCVFVGHGLNNDFKHININVPRnqIRDTAIYFL------QGKRYLSLRYLAYVLLGM 616
Cdd:cd06137    61 AKAGKTIFGWEAARAaLWKFIDPDTILVGHSLQNDLDALRMIHTR--VVDTAILTReavkgpLAKRQWSLRTLCRDFLGL 138
                         170       180
                  ....*....|....*....|..
gi 1679885188 617 NIQEGN--HDSIEDAHTALILY 636
Cdd:cd06137   139 KIQGGGegHDSLEDALAAREVV 160
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
464-636 8.79e-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: 95.50  E-value: 8.79e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 464 VAIDAAFVSLQselceidhqgirsIIRPKRTALARISIIRGEEGElygVPFVDDYVVNT--NHIEDYLTRYSGILPGDLD 541
Cdd:pfam00929   1 VVIDLETTGLD-------------PEKDEIIEIAAVVIDGGENEI---GETFHTYVKPTrlPKLTDECTKFTGITQAMLD 64
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 542 PEKSTK-RLVRRNVVYRKVWLLMQLG-CVFVGHGLNNDFKHININVP-RNQIRDTAIYF---LQGKRYLSLRYLAYVLLG 615
Cdd:pfam00929  65 NKPSFEeVLEEFLEFLRKGNLLVAHNaSFDVGFLRYDDKRFLKKPMPkLNPVIDTLILDkatYKELPGRSLDALAEKLGL 144
                         170       180
                  ....*....|....*....|.
gi 1679885188 616 MNIQEgNHDSIEDAHTALILY 636
Cdd:pfam00929 145 EHIGR-AHRALDDARATAKLF 164
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
495-633 1.68e-21

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: 91.39  E-value: 1.68e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 495 ALARISIIrGEEGELygvpFVDDYVVNTNHIEDYLTRYSGILPGDLDPEKSTKRLVRRNvvyrkvwLLMQLGC--VFVGH 572
Cdd:cd06145    15 ELTRVTVV-DENGKV----VLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKK-------LLSLISPdtILVGH 82
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1679885188 573 GLNNDFKHININVPRnqIRDTAIYFL--QGKRY-LSLRYLAYVLLGMNIQ--EGNHDSIEDAHTAL 633
Cdd:cd06145    83 SLENDLKALKLIHPR--VIDTAILFPhpRGPPYkPSLKNLAKKYLGRDIQqgEGGHDSVEDARAAL 146
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
492-637 2.11e-18

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: 82.49  E-value: 2.11e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 492 KRTALARISIIRGEEGELYgvpfvDDYVVNTNHIEDYLTRYSGILPGDLdpEKSTKRLVRRNVVyrkvwLLMQLGCVFVG 571
Cdd:cd06149    15 RESELARCSIVNYHGDVLY-----DKYIRPEGPVTDYRTRWSGIRRQHL--VNATPFAVAQKEI-----LKILKGKVVVG 82
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1679885188 572 HGLNNDFKHININVPRNQIRDTA-------IYFLQGKRYLSLRYLAYVLLGMNIQEG--NHDSIEDAHTALILYK 637
Cdd:cd06149    83 HAIHNDFKALKYFHPKHMTRDTStipllnrKAGFPENCRVSLKVLAKRLLHRDIQVGrqGHSSVEDARATMELYK 157
Peptidase_C19 cd02257
Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ...
176-409 1.87e-04

Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.


Pssm-ID: 239072 [Multi-domain]  Cd Length: 255  Bit Score: 43.63  E-value: 1.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 176 PQKFNRFLLSQLIKEEAQTVNHNI-------TLNQCFGLETEIRTEC-SCDHYDTTVKLLPSLSIS-----GINKTVIKQ 242
Cdd:cd02257    25 AHEFLLFLLDKLHEELKKSSKRTSdssslksLIHDLFGGKLESTIVClECGHESVSTEPELFLSLPlpvkgLPQVSLEDC 104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 243 LNKKSNGQNILPYIEYAmknvtqknsiCPTCGKTETITQEC----------TVKNLPSVLSLELSLLDTEFSnirssknw 312
Cdd:cd02257   105 LEKFFKEEILEGDNCYK----------CEKKKKQEATKRLKikklppvliiHLKRFSFNEDGTKEKLNTKVS-------- 166
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1679885188 313 ltsefYGSIIKNKAVLRSTASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVKKYNPKencfKWLMFNDYLVVEITEE 392
Cdd:cd02257   167 -----FPLELDLSPYLSEGEKDSDSDNGSYKYELVAVVVHSGTSADSGHYVAYVKDPSDG----KWYKFNDDKVTEVSEE 237
                         250
                  ....*....|....*..
gi 1679885188 393 EALKMTYPWKTPEIIIY 409
Cdd:cd02257   238 EVLEFGSLSSSAYILFY 254
 
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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