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Conserved domains on  [gi|6319647|ref|NP_009729|]
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nuclear protein localization protein 4 [Saccharomyces cerevisiae S288C]

Protein Classification

nuclear protein localization protein 4( domain architecture ID 11473805)

nuclear protein localization protein 4 (NPL4) is involved in the import of nuclear-targeted proteins into the nucleus and the export of poly(A) RNA out of the nucleus

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
1-580 0e+00

Nuclear pore protein [Nuclear structure];


:

Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 1022.24  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    1 MLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKP-GQGIhAVSELADRTVMDLGLKHGDMLILNYS 79
Cdd:COG5100   1 MIFRFRSKEGQRRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPdGQGE-IFSLLKDQTPDDLGLRHGQMLYLEYS 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647   80 DKPANEKDGVNVEIGSVGIDSKGIRQHRYGpLRIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYH 159
Cdd:COG5100  80 DIASNNEKKRDVPGKPKQDCSKGIKREKDS-MPVIQDPIDDSLEKEDGLIRRSMTMLCQHGSNGMCSYCSPLDPWDEKYY 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  160 EKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEF 239
Cdd:COG5100 159 KDNKIKHLSFHSYLEKMNSNKNKLGSVESYIVPLEEPSFTVKETCEDGHGPWPHGICNKCQPSNIILAPQVFRMVDHVEF 238
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  240 QKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMdvEQVKNEMLqIDRQAQEMGL 319
Cdd:COG5100 239 DGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTI--EEWADEGL-MDAPASGTGL 315
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  320 SRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSY 399
Cdd:COG5100 316 ERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGLQSY 395
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  400 QVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPntdTETNS 479
Cdd:COG5100 396 QVSNQCMALVKADYILPSEDPRRFLATKEDQTRYVPDIFYRYTDTYGEEVMENAKPAFPVEFLLVTLTHGFP---EKPNP 472
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  480 KFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASsgDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIESAVKNEWEES 559
Cdd:COG5100 473 LFRSIDFIPKKFGDRKMAEYFGGDLSKELFSNFT--LLTRIQGVFSNFKDLLKIIVLRILDKFDFKSFISSMERYRWECK 550
                       570       580
                ....*....|....*....|.
gi 6319647  560 LLKLVSSAGWQTLVMILQESG 580
Cdd:COG5100 551 MCTFINEKNSCTCEMCNSTRD 571
 
Name Accession Description Interval E-value
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
1-580 0e+00

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 1022.24  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    1 MLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKP-GQGIhAVSELADRTVMDLGLKHGDMLILNYS 79
Cdd:COG5100   1 MIFRFRSKEGQRRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPdGQGE-IFSLLKDQTPDDLGLRHGQMLYLEYS 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647   80 DKPANEKDGVNVEIGSVGIDSKGIRQHRYGpLRIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYH 159
Cdd:COG5100  80 DIASNNEKKRDVPGKPKQDCSKGIKREKDS-MPVIQDPIDDSLEKEDGLIRRSMTMLCQHGSNGMCSYCSPLDPWDEKYY 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  160 EKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEF 239
Cdd:COG5100 159 KDNKIKHLSFHSYLEKMNSNKNKLGSVESYIVPLEEPSFTVKETCEDGHGPWPHGICNKCQPSNIILAPQVFRMVDHVEF 238
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  240 QKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMdvEQVKNEMLqIDRQAQEMGL 319
Cdd:COG5100 239 DGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTI--EEWADEGL-MDAPASGTGL 315
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  320 SRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSY 399
Cdd:COG5100 316 ERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGLQSY 395
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  400 QVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPntdTETNS 479
Cdd:COG5100 396 QVSNQCMALVKADYILPSEDPRRFLATKEDQTRYVPDIFYRYTDTYGEEVMENAKPAFPVEFLLVTLTHGFP---EKPNP 472
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  480 KFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASsgDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIESAVKNEWEES 559
Cdd:COG5100 473 LFRSIDFIPKKFGDRKMAEYFGGDLSKELFSNFT--LLTRIQGVFSNFKDLLKIIVLRILDKFDFKSFISSMERYRWECK 550
                       570       580
                ....*....|....*....|.
gi 6319647  560 LLKLVSSAGWQTLVMILQESG 580
Cdd:COG5100 551 MCTFINEKNSCTCEMCNSTRD 571
NPL4 pfam05021
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
259-577 0e+00

NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.


Pssm-ID: 461524  Cd Length: 309  Bit Score: 578.84  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    259 RFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMdveQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGS 338
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITL---LPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGT 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    339 VFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGST 418
Cdd:pfam05021  78 VLCKRHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPST 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    419 FPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPntdTETNSKFVSSTGFPWSNRQAMGQS 498
Cdd:pfam05021 158 DPSVAYVRESSDERYVPEVFYSKINEYGLEVKENAKPAFPVEYLLVTLTHGFP---LEPSPTFSANNGFPIENREAMGEL 234
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6319647    499 QDYQELKKYLFnvaSSGDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIEsAVKNEWEESLLKLVSSAGWQTLVMILQ 577
Cdd:pfam05021 235 QDLSALAKYLK---SSADPNDFLEALSNFHLLLYLHSLGILSKDEESLLCR-AATQKDTEDLLQLIESPGWQTLVTILQ 309
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
225-533 3.13e-101

Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.


Pssm-ID: 163692  Cd Length: 274  Bit Score: 307.75  E-value: 3.13e-101
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  225 TLQQQEFRMVDHVEFQKSEIINEFIQA-WRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMdVEqv 303
Cdd:cd08061   1 TLKRQKYRHVDHVEFDNPSIVEFFLYVfWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFEL-LE-- 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  304 KNEMLQIDRQAQEMGLSRIGLIFTDLSDagagdgsvfckRHKDSFFLSSLEVIMAARHQTRHPNvskyseqGFFSSKFVT 383
Cdd:cd08061  78 DPNADTVDAIAAALGLERVGWIFTDLPR-----------EDKDGYFLSAEEVILAAKFQLKHPT-------GKFGSKFVT 139
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  384 CVISGNLEGEIDISSYQVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITvkeNAKPAFPVDYLL 463
Cdd:cd08061 140 VVVTGDKDGQIHFEAYQVSDQAMALVRDGLLLPTKDADELYVREPTLERYVPDVFYSGKDKYGKT---KAVPEVDVEYFL 216
                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6319647  464 VTLTHGFPntdteTNSKFVSSTGFPWSNRQA-MGQSQDYQELKKYLFNVassgdfnlLHEKISNFHLLLYI 533
Cdd:cd08061 217 VDVPHGFP-----LSPSSFKSSDFPIENRPPsLGELQDLDALARYLGKP--------FLERLSDFHLLLYL 274
 
Name Accession Description Interval E-value
NPL4 COG5100
Nuclear pore protein [Nuclear structure];
1-580 0e+00

Nuclear pore protein [Nuclear structure];


Pssm-ID: 227431 [Multi-domain]  Cd Length: 571  Bit Score: 1022.24  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    1 MLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKP-GQGIhAVSELADRTVMDLGLKHGDMLILNYS 79
Cdd:COG5100   1 MIFRFRSKEGQRRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPdGQGE-IFSLLKDQTPDDLGLRHGQMLYLEYS 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647   80 DKPANEKDGVNVEIGSVGIDSKGIRQHRYGpLRIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYH 159
Cdd:COG5100  80 DIASNNEKKRDVPGKPKQDCSKGIKREKDS-MPVIQDPIDDSLEKEDGLIRRSMTMLCQHGSNGMCSYCSPLDPWDEKYY 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  160 EKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEF 239
Cdd:COG5100 159 KDNKIKHLSFHSYLEKMNSNKNKLGSVESYIVPLEEPSFTVKETCEDGHGPWPHGICNKCQPSNIILAPQVFRMVDHVEF 238
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  240 QKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMdvEQVKNEMLqIDRQAQEMGL 319
Cdd:COG5100 239 DGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTI--EEWADEGL-MDAPASGTGL 315
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  320 SRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSY 399
Cdd:COG5100 316 ERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGLQSY 395
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  400 QVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPntdTETNS 479
Cdd:COG5100 396 QVSNQCMALVKADYILPSEDPRRFLATKEDQTRYVPDIFYRYTDTYGEEVMENAKPAFPVEFLLVTLTHGFP---EKPNP 472
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  480 KFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASsgDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIESAVKNEWEES 559
Cdd:COG5100 473 LFRSIDFIPKKFGDRKMAEYFGGDLSKELFSNFT--LLTRIQGVFSNFKDLLKIIVLRILDKFDFKSFISSMERYRWECK 550
                       570       580
                ....*....|....*....|.
gi 6319647  560 LLKLVSSAGWQTLVMILQESG 580
Cdd:COG5100 551 MCTFINEKNSCTCEMCNSTRD 571
NPL4 pfam05021
NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear ...
259-577 0e+00

NPL4 family; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.


Pssm-ID: 461524  Cd Length: 309  Bit Score: 578.84  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    259 RFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMdveQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGS 338
Cdd:pfam05021   1 RFGYLYGRYEEYDEVPLGIKAVVEAIYEPPQHDELDGITL---LPWENEKDVDEIARELGLERVGVIFTDLTDAGAGDGT 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    339 VFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGST 418
Cdd:pfam05021  78 VLCKRHKDSYFLSSLEVIMAARLQARHPNPTKYSETGRFGSKFVTCVVSGDLNGEIDISSYQVSNQAEALVRADIIEPST 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    419 FPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPntdTETNSKFVSSTGFPWSNRQAMGQS 498
Cdd:pfam05021 158 DPSVAYVRESSDERYVPEVFYSKINEYGLEVKENAKPAFPVEYLLVTLTHGFP---LEPSPTFSANNGFPIENREAMGEL 234
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6319647    499 QDYQELKKYLFnvaSSGDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIEsAVKNEWEESLLKLVSSAGWQTLVMILQ 577
Cdd:pfam05021 235 QDLSALAKYLK---SSADPNDFLEALSNFHLLLYLHSLGILSKDEESLLCR-AATQKDTEDLLQLIESPGWQTLVTILQ 309
MPN_NPL4 cd08061
Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein ...
225-533 3.13e-101

Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain; Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.


Pssm-ID: 163692  Cd Length: 274  Bit Score: 307.75  E-value: 3.13e-101
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  225 TLQQQEFRMVDHVEFQKSEIINEFIQA-WRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMdVEqv 303
Cdd:cd08061   1 TLKRQKYRHVDHVEFDNPSIVEFFLYVfWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFEL-LE-- 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  304 KNEMLQIDRQAQEMGLSRIGLIFTDLSDagagdgsvfckRHKDSFFLSSLEVIMAARHQTRHPNvskyseqGFFSSKFVT 383
Cdd:cd08061  78 DPNADTVDAIAAALGLERVGWIFTDLPR-----------EDKDGYFLSAEEVILAAKFQLKHPT-------GKFGSKFVT 139
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  384 CVISGNLEGEIDISSYQVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITvkeNAKPAFPVDYLL 463
Cdd:cd08061 140 VVVTGDKDGQIHFEAYQVSDQAMALVRDGLLLPTKDADELYVREPTLERYVPDVFYSGKDKYGKT---KAVPEVDVEYFL 216
                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6319647  464 VTLTHGFPntdteTNSKFVSSTGFPWSNRQA-MGQSQDYQELKKYLFNVassgdfnlLHEKISNFHLLLYI 533
Cdd:cd08061 217 VDVPHGFP-----LSPSSFKSSDFPIENRPPsLGELQDLDALARYLGKP--------FLERLSDFHLLLYL 274
zf-NPL4 pfam05020
NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene ...
113-256 1.27e-99

NPL4 family, putative zinc binding region; The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. This region of the protein contains possibly two zinc binding motifs (Bateman A pers. obs.). Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.


Pssm-ID: 461523  Cd Length: 145  Bit Score: 298.35  E-value: 1.27e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647    113 IKELAVDEELEKEDGLIPRQKS-KLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLNENANKKENGSSYIS 191
Cdd:pfam05020   1 VKEDPVDDYLDKQDGKIPRKRDpKLCRHGPKGMCDYCSPLEPYDEEYLKEHKIKHLSFHAYLRKLNSGTNKKESGSSYIP 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6319647    192 PLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQKSEIINEFIQAWRYTG 256
Cdd:pfam05020  81 PLEEPSYKVKPGCPSGHPPWPKGICSKCQPSAITLQRQPFRMVDHVEFANSEIVNRFLDFWRKTG 145
Ubl_AtNPL4_like cd17055
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ...
1-77 1.14e-11

ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, and similar proteins; The family includes a group of uncharacterized plant ubiquitin-like (Ubl) domain-containing proteins, including Arabidopsis thaliana NPL4-like protein 1 and NPL4-like protein 2.


Pssm-ID: 340575  Cd Length: 73  Bit Score: 60.31  E-value: 1.14e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6319647    1 MLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNadVDTFTVCEKPGQGIhaVSELADRTVMDLGLKHGDMLILN 77
Cdd:cd17055   1 MLLRVRSRDGTERVEVPDDATVGDLKEKIAEQLSVP--VSDQTLSLDPGPDL--LTAKSSATLSQLGLKHGDMVFLS 73
MPN cd07767
Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) ...
248-367 1.69e-03

Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function.


Pssm-ID: 163686 [Multi-domain]  Cd Length: 116  Bit Score: 38.65  E-value: 1.69e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319647  248 FIQAWRY-TGMQRFGYMYGSYSKYdntpLGIKAVVEAIYEPPQHDeqdglTMDVEQVKnemlQIDRQAQEMGLSRIGLIF 326
Cdd:cd07767   4 FLDAAKSiNGKEVIGLLYGSKTKK----VLDVDEVIAVPFDEGDK-----DDNVWFLM----YLDFKKLNAGLRIVGWYH 70
                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 6319647  327 TDLsdagagdgsvfckrhKDSFFLSSLEVIMAARHQTRHPN 367
Cdd:cd07767  71 THP---------------KPSCFLSPNDLATHELFQRYFPE 96
 
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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