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Conserved domains on  [gi|19920838|ref|NP_609060|]
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ubiquitination factor E4A [Drosophila melanogaster]

Protein Classification

ubiquitin conjugation factor E4( domain architecture ID 12105733)

ubiquitin conjugation factor E4 is a ubiquitin-protein ligase that probably functions as an E3 ligase in conjunction with specific E1 and E2 ligases, and may also function as an E4 ligase mediating the assembly of polyubiquitin chains on substrates ubiquitinated by another E3 ubiquitin ligase

CATH:  3.30.40.10
EC:  2.3.2.-
Gene Ontology:  GO:0006511|GO:0000209|GO:0034450
SCOP:  3000160

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Ufd2P_core pfam10408
Ubiquitin elongating factor core; This is the most conserved part of the core region of Ufd2P ...
251-898 0e+00

Ubiquitin elongating factor core; This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, pfam04564, which has ligase activity.


:

Pssm-ID: 463080  Cd Length: 594  Bit Score: 558.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   251 LGSLLCISILPKTQTGKYEFFQELS------INQTDEALWALLSHHQQSIFLLVKQLLVLSPETKKKTLQWVGNCLDANV 324
Cdd:pfam10408   1 LGPFLRLSPLPDDPEVAKKYFSNPKtrspadIESSQSSLRQELKTLQEQLFQIVNKLLRASPESRERVLDWFAQIINLNH 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   325 PRGHLWSSINasleqtahSTSSDAFMTNLTAVLVRLCAPLCMPS-LKVLLVDPTYCAVPNkdrqakgvSMLRAHAETCLL 403
Cdd:pfam10408  81 KRRKMQVDPN--------TVSSDGFMLNLTAVLLRLCEPFLDATfSKIDKIDPDYLLPRS--------SRIDISDETRLN 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   404 -TSEEGEE----RLTAEKYNFVTEIFYMTHKCFELSNIPCIERFVRVLRELQNTQMaygeivnsdpnsevaknlfrmird 478
Cdd:pfam10408 145 aDQEEADEfyeqKAKEGEPNFITECFFLTLAALHLGILPAISKYKRLARELKRLQA------------------------ 200
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   479 qiqQVLTIKNTLAEPTNDMYLLKFFEASAIWLTEIAmlpreiyeqclDKRDFSPQVFRNMELLSDTPPfvapYMQSVPES 558
Cdd:pfam10408 201 ---EKLAYEAVLLDPSLLQRSLQFLRFVATWLLRVA-----------DPKHQYPKKPLKLPLPAEPPE----PFKYLPEY 262
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   559 IIDNISAFLNAARKLNGEQYINIYFSahDAFFKMIILFMGSSALVKNPHLRAKLAEALEFLLPSriMGSHRKTFVSHVFD 638
Cdd:pfam10408 263 FIEDIVDFLLFVTRFAPDILESLSQL--DELITFCIVFLRSPEYIKNPHLKAKLVEVLFYGTPP--RQNGRPGVLGDILE 338
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   639 NHPDRLK-VVRSLLNVFVSIEMTGQSVQFEQKFNYRRPMYAIMEFLWTKPEHVQCFRDlavEAEQNMDaieppIFLRFIN 717
Cdd:pfam10408 339 SHPLALKhLLPALMKFYIDVEKTGASSQFYDKFNIRYNISQILKYLWKNPSYREQLKK---EAKENED-----FFVRFVN 410
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   718 LLINDAIFLLDESLSNLEQIKQLQQAQDN-GEWESLPHTEREQHMTNLQHLGMLARFDNIIGRDTINLLKLLTSKIKSIF 796
Cdd:pfam10408 411 LLLNDVTFLLDESLSKLKEIHELQEEMADaAEWEALPEEERQEREEQLRSLERQAKSYLQLANETVKLLKLFTKEIPEPF 490
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   797 CHNSMVDRMAAMLNYFLLNLVGPKKERFKVKDKKEFEFDPAQTVIEISHIYINLSSDESFCLAVSQDGRSYSEQLFSYAE 876
Cdd:pfam10408 491 LMPEIVDRLAAMLNYNLDQLVGPKCKNLKVKNPEKYGFNPKELLSDIVDIYLNLSDQPEFVRAVARDGRSYSPELFEKAA 570
                         650       660
                  ....*....|....*....|....
gi 19920838   877 NILIRIGGGQL--IGDMSEFAVKV 898
Cdd:pfam10408 571 RILRRKGLKSPeeIEKFEELAQKV 594
RING-Ubox_UBE4A cd16657
U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and ...
917-986 7.60e-41

U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and similar proteins; This subfamily includes yeast ubiquitin fusion degradation protein 2 (UFD2p) and its mammalian homolog, UBE4A. Yeast UFD2p, also known as ubiquitin conjugation factor E4 or UB fusion protein 2, is a polyubiquitin chain conjugation factor (E4) in the ubiquitin fusion degradation (UFD) pathway which catalyzes elongation of the ubiquitin chain through Lys48 linkage. It binds to substrates conjugated with one to three ubiquitin molecules and catalyzes the addition of further ubiquitin moieties in the presence of ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3), yielding multiubiquitylated substrates that are targets for the 26S proteasome. UFD2p is implicated in cell survival under stress conditions and is essential for homoeostasis of unsaturated fatty acids. It interacts with UBL-UBA proteins Rad23 and Dsk2, which are involved in the endoplasmic reticulum-associated degradation, ubiquitin fusion degradation, and OLE-1 gene induction pathways. UBE4A is a U-box-type ubiquitin-protein ligase that is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. It may have a specific role in different biochemical processes other than ubiquitination, including growth or differentiation. Members of this family contain an N-terminal ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus.


:

Pssm-ID: 438319  Cd Length: 70  Bit Score: 144.34  E-value: 7.60e-41
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 917 EEYLDPIISTLMTDPVVLPSSKVTVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEALKQEIESWIQGKR 986
Cdd:cd16657   1 DEFLDPIMYTLMKDPVILPSSKVTVDRSTIKRHLLSDQTDPFNRSPLTLDMVIPNEELKQKIEEFLAEKK 70
 
Name Accession Description Interval E-value
Ufd2P_core pfam10408
Ubiquitin elongating factor core; This is the most conserved part of the core region of Ufd2P ...
251-898 0e+00

Ubiquitin elongating factor core; This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, pfam04564, which has ligase activity.


Pssm-ID: 463080  Cd Length: 594  Bit Score: 558.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   251 LGSLLCISILPKTQTGKYEFFQELS------INQTDEALWALLSHHQQSIFLLVKQLLVLSPETKKKTLQWVGNCLDANV 324
Cdd:pfam10408   1 LGPFLRLSPLPDDPEVAKKYFSNPKtrspadIESSQSSLRQELKTLQEQLFQIVNKLLRASPESRERVLDWFAQIINLNH 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   325 PRGHLWSSINasleqtahSTSSDAFMTNLTAVLVRLCAPLCMPS-LKVLLVDPTYCAVPNkdrqakgvSMLRAHAETCLL 403
Cdd:pfam10408  81 KRRKMQVDPN--------TVSSDGFMLNLTAVLLRLCEPFLDATfSKIDKIDPDYLLPRS--------SRIDISDETRLN 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   404 -TSEEGEE----RLTAEKYNFVTEIFYMTHKCFELSNIPCIERFVRVLRELQNTQMaygeivnsdpnsevaknlfrmird 478
Cdd:pfam10408 145 aDQEEADEfyeqKAKEGEPNFITECFFLTLAALHLGILPAISKYKRLARELKRLQA------------------------ 200
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   479 qiqQVLTIKNTLAEPTNDMYLLKFFEASAIWLTEIAmlpreiyeqclDKRDFSPQVFRNMELLSDTPPfvapYMQSVPES 558
Cdd:pfam10408 201 ---EKLAYEAVLLDPSLLQRSLQFLRFVATWLLRVA-----------DPKHQYPKKPLKLPLPAEPPE----PFKYLPEY 262
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   559 IIDNISAFLNAARKLNGEQYINIYFSahDAFFKMIILFMGSSALVKNPHLRAKLAEALEFLLPSriMGSHRKTFVSHVFD 638
Cdd:pfam10408 263 FIEDIVDFLLFVTRFAPDILESLSQL--DELITFCIVFLRSPEYIKNPHLKAKLVEVLFYGTPP--RQNGRPGVLGDILE 338
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   639 NHPDRLK-VVRSLLNVFVSIEMTGQSVQFEQKFNYRRPMYAIMEFLWTKPEHVQCFRDlavEAEQNMDaieppIFLRFIN 717
Cdd:pfam10408 339 SHPLALKhLLPALMKFYIDVEKTGASSQFYDKFNIRYNISQILKYLWKNPSYREQLKK---EAKENED-----FFVRFVN 410
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   718 LLINDAIFLLDESLSNLEQIKQLQQAQDN-GEWESLPHTEREQHMTNLQHLGMLARFDNIIGRDTINLLKLLTSKIKSIF 796
Cdd:pfam10408 411 LLLNDVTFLLDESLSKLKEIHELQEEMADaAEWEALPEEERQEREEQLRSLERQAKSYLQLANETVKLLKLFTKEIPEPF 490
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   797 CHNSMVDRMAAMLNYFLLNLVGPKKERFKVKDKKEFEFDPAQTVIEISHIYINLSSDESFCLAVSQDGRSYSEQLFSYAE 876
Cdd:pfam10408 491 LMPEIVDRLAAMLNYNLDQLVGPKCKNLKVKNPEKYGFNPKELLSDIVDIYLNLSDQPEFVRAVARDGRSYSPELFEKAA 570
                         650       660
                  ....*....|....*....|....
gi 19920838   877 NILIRIGGGQL--IGDMSEFAVKV 898
Cdd:pfam10408 571 RILRRKGLKSPeeIEKFEELAQKV 594
UFD2 COG5113
Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, ...
162-990 5.59e-84

Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227444 [Multi-domain]  Cd Length: 929  Bit Score: 291.50  E-value: 5.59e-84
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 162 EFLIRVTCKVMEEVEPIEALgalkaiFYPVLTELQKNIAKLNLITMKKNTFWILGYFVRDKRAAVLgELLIDYTTPNPRA 241
Cdd:COG5113 133 IFLSSFKQRQLDEASNLDNL------FTSALEALTGLHGVLEEDTVLKNVMEIYWGLVNTKPIADV-ILKFPIYSGTNFP 205
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 242 SGSEYMdTLLGSLLciSILPKTQTGKYEFFQELSINQTD------EALWALLSHHQQSIFLLVKQLLVLSPETKKKTLQW 315
Cdd:COG5113 206 CGFEYK-TLLGFIE--SLSYKKCDVAARALDYLGIRSRQvveksrRSLRLTLSDHSDKLFQIIHSLVRSSKELRANFMKY 282
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 316 VGNCLDANvprgHLWSSINASLEQTahstSSDAFMTNLTAVLVRLCAP-LCMPSLKVLLVDPTYCAVPNKDrqAKGVSML 394
Cdd:COG5113 283 FAKVINVN----HERSKTIFSWREN----ISDGFMYNMSMVLSRFSRPfLDIGCSKIDMVDKIYFNNPRVD--IKEETKL 352
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 395 RAHAETclltSEEGEERLTAEKYNFVTEIFYMT---HKCFELSNIPCIERFVRVLRELQNT-----QMAYGEIVNSDPNS 466
Cdd:COG5113 353 NVDEKS----LDSFYTKPAEGSNNFISDIFFLYltkIHYGVNATFTSCEKFGEYIRKLKESleyecRLLDGSFQATRLTA 428
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 467 -----EVAKNLFRMIRDQIQQVLTIKNTLAEptndmyLLKFFEASAIWLTEIAmlpreiyeqclDKRDFSPQVFRNMELL 541
Cdd:COG5113 429 qlsrmEAYLKGIDSKMSALNGFLFMTSLFAD------EFPFTDFMTEYLARVE-----------DPWPTYPFYYKTLPWM 491
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 542 SDTP-PFvapymQSVPESIIDNIsafLNAARKLNGEQYINIYFSAHDAFFKMIILFMGSSALVKNPHLRAKLAEALEFLL 620
Cdd:COG5113 492 ENAPmTF-----KLIPEATIENA---LNYVLESIKDWRSPIFKKELEPLCEFVKIVLHRSSAIKNPMLNRKLDYYLSLGR 563
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 621 PSRIMGShrKTFVSHVFDNhpDRL---KVVRSLLNVFVSIEMTGQSVQFEQKFNYRRPMYAIMEFLWTKPEHvqcFRDLA 697
Cdd:COG5113 564 DEMRMES--RSIIHDIFKE--GKVfsrWLLPALMAFYIEIESTGQSTQFYDKFNIRFIICMMKDFEYKQPSY---SEGLS 636
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 698 VEAEQNMdaiepPIFLRFINLLINDAIFLLDESLSNLEQIKQLQQAQDNGEWESLPHTEREQHMTNLQHLGMLARFDNII 777
Cdd:COG5113 637 SIKDTNL-----PFFVKFDAKMLNDLTRLLDEALKELVEEHNIQSLLADAISNSNISERIGELQKSLAFAKRQARNSCLL 711
                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 778 GRDTINLLKLLTSKIKSIFCHNSMVDRMAAMLNYFLLNLVGPKKERFKVKDKKEFEFDPAQTVIEISHIYINLSSDESFC 857
Cdd:COG5113 712 VDGCFDLFTHILDEIPDAFLVDEIVSRLARMLNYNLKILTGPKCTDLKVKDPEQYGFNAKNLLRRMVMVYINLRSESKFV 791
                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 858 LAVSQDGRSYSEQLFSYAENILIR--IGGGQLIGDMSEFAVKVARMGAQYKEEQELLADAPEEYLDPIISTLMTDPVVLP 935
Cdd:COG5113 792 EAVASDKRSFDIDFFRRALRICENkyLISESQIEELRSFINRLEKVRVIEAVEEEDMGDVPDEFLDPLMFTIMKDPVKLP 871
                       810       820       830       840       850
                ....*....|....*....|....*....|....*....|....*....|....*
gi 19920838 936 SSKVTVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEALKQEIESWIQGKREAAR 990
Cdd:COG5113 872 TSRITIDRSTIKAHLLSDGTDPFNRMPLTLDDVTPNAELREKINRFYKCKGQKHG 926
RING-Ubox_UBE4A cd16657
U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and ...
917-986 7.60e-41

U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and similar proteins; This subfamily includes yeast ubiquitin fusion degradation protein 2 (UFD2p) and its mammalian homolog, UBE4A. Yeast UFD2p, also known as ubiquitin conjugation factor E4 or UB fusion protein 2, is a polyubiquitin chain conjugation factor (E4) in the ubiquitin fusion degradation (UFD) pathway which catalyzes elongation of the ubiquitin chain through Lys48 linkage. It binds to substrates conjugated with one to three ubiquitin molecules and catalyzes the addition of further ubiquitin moieties in the presence of ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3), yielding multiubiquitylated substrates that are targets for the 26S proteasome. UFD2p is implicated in cell survival under stress conditions and is essential for homoeostasis of unsaturated fatty acids. It interacts with UBL-UBA proteins Rad23 and Dsk2, which are involved in the endoplasmic reticulum-associated degradation, ubiquitin fusion degradation, and OLE-1 gene induction pathways. UBE4A is a U-box-type ubiquitin-protein ligase that is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. It may have a specific role in different biochemical processes other than ubiquitination, including growth or differentiation. Members of this family contain an N-terminal ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus.


Pssm-ID: 438319  Cd Length: 70  Bit Score: 144.34  E-value: 7.60e-41
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 917 EEYLDPIISTLMTDPVVLPSSKVTVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEALKQEIESWIQGKR 986
Cdd:cd16657   1 DEFLDPIMYTLMKDPVILPSSKVTVDRSTIKRHLLSDQTDPFNRSPLTLDMVIPNEELKQKIEEFLAEKK 70
U-box pfam04564
U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast ...
915-987 9.12e-32

U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.


Pssm-ID: 398320 [Multi-domain]  Cd Length: 73  Bit Score: 118.18  E-value: 9.12e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19920838   915 APEEYLDPIISTLMTDPVVLPSSkVTVDRSTIARHLLS-DQTDPFNREPLTMDKVKSNEALKQEIESWIQGKRE 987
Cdd:pfam04564   1 IPDEFLDPITFELMTDPVILPSG-ITYDRSTIERHLLSvDPTDPFTREPLTHDQLIPNLELKAKIDAWLEEKRW 73
Ubox smart00504
Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2 ...
918-981 1.26e-19

Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.


Pssm-ID: 128780 [Multi-domain]  Cd Length: 63  Bit Score: 83.44  E-value: 1.26e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19920838    918 EYLDPIISTLMTDPVVLPSSkVTVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEALKQEIESW 981
Cdd:smart00504   1 EFLCPISLEVMKDPVILPSG-QTYERSAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQEW 63
 
Name Accession Description Interval E-value
Ufd2P_core pfam10408
Ubiquitin elongating factor core; This is the most conserved part of the core region of Ufd2P ...
251-898 0e+00

Ubiquitin elongating factor core; This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, pfam04564, which has ligase activity.


Pssm-ID: 463080  Cd Length: 594  Bit Score: 558.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   251 LGSLLCISILPKTQTGKYEFFQELS------INQTDEALWALLSHHQQSIFLLVKQLLVLSPETKKKTLQWVGNCLDANV 324
Cdd:pfam10408   1 LGPFLRLSPLPDDPEVAKKYFSNPKtrspadIESSQSSLRQELKTLQEQLFQIVNKLLRASPESRERVLDWFAQIINLNH 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   325 PRGHLWSSINasleqtahSTSSDAFMTNLTAVLVRLCAPLCMPS-LKVLLVDPTYCAVPNkdrqakgvSMLRAHAETCLL 403
Cdd:pfam10408  81 KRRKMQVDPN--------TVSSDGFMLNLTAVLLRLCEPFLDATfSKIDKIDPDYLLPRS--------SRIDISDETRLN 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   404 -TSEEGEE----RLTAEKYNFVTEIFYMTHKCFELSNIPCIERFVRVLRELQNTQMaygeivnsdpnsevaknlfrmird 478
Cdd:pfam10408 145 aDQEEADEfyeqKAKEGEPNFITECFFLTLAALHLGILPAISKYKRLARELKRLQA------------------------ 200
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   479 qiqQVLTIKNTLAEPTNDMYLLKFFEASAIWLTEIAmlpreiyeqclDKRDFSPQVFRNMELLSDTPPfvapYMQSVPES 558
Cdd:pfam10408 201 ---EKLAYEAVLLDPSLLQRSLQFLRFVATWLLRVA-----------DPKHQYPKKPLKLPLPAEPPE----PFKYLPEY 262
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   559 IIDNISAFLNAARKLNGEQYINIYFSahDAFFKMIILFMGSSALVKNPHLRAKLAEALEFLLPSriMGSHRKTFVSHVFD 638
Cdd:pfam10408 263 FIEDIVDFLLFVTRFAPDILESLSQL--DELITFCIVFLRSPEYIKNPHLKAKLVEVLFYGTPP--RQNGRPGVLGDILE 338
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   639 NHPDRLK-VVRSLLNVFVSIEMTGQSVQFEQKFNYRRPMYAIMEFLWTKPEHVQCFRDlavEAEQNMDaieppIFLRFIN 717
Cdd:pfam10408 339 SHPLALKhLLPALMKFYIDVEKTGASSQFYDKFNIRYNISQILKYLWKNPSYREQLKK---EAKENED-----FFVRFVN 410
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   718 LLINDAIFLLDESLSNLEQIKQLQQAQDN-GEWESLPHTEREQHMTNLQHLGMLARFDNIIGRDTINLLKLLTSKIKSIF 796
Cdd:pfam10408 411 LLLNDVTFLLDESLSKLKEIHELQEEMADaAEWEALPEEERQEREEQLRSLERQAKSYLQLANETVKLLKLFTKEIPEPF 490
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838   797 CHNSMVDRMAAMLNYFLLNLVGPKKERFKVKDKKEFEFDPAQTVIEISHIYINLSSDESFCLAVSQDGRSYSEQLFSYAE 876
Cdd:pfam10408 491 LMPEIVDRLAAMLNYNLDQLVGPKCKNLKVKNPEKYGFNPKELLSDIVDIYLNLSDQPEFVRAVARDGRSYSPELFEKAA 570
                         650       660
                  ....*....|....*....|....
gi 19920838   877 NILIRIGGGQL--IGDMSEFAVKV 898
Cdd:pfam10408 571 RILRRKGLKSPeeIEKFEELAQKV 594
UFD2 COG5113
Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, ...
162-990 5.59e-84

Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227444 [Multi-domain]  Cd Length: 929  Bit Score: 291.50  E-value: 5.59e-84
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 162 EFLIRVTCKVMEEVEPIEALgalkaiFYPVLTELQKNIAKLNLITMKKNTFWILGYFVRDKRAAVLgELLIDYTTPNPRA 241
Cdd:COG5113 133 IFLSSFKQRQLDEASNLDNL------FTSALEALTGLHGVLEEDTVLKNVMEIYWGLVNTKPIADV-ILKFPIYSGTNFP 205
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 242 SGSEYMdTLLGSLLciSILPKTQTGKYEFFQELSINQTD------EALWALLSHHQQSIFLLVKQLLVLSPETKKKTLQW 315
Cdd:COG5113 206 CGFEYK-TLLGFIE--SLSYKKCDVAARALDYLGIRSRQvveksrRSLRLTLSDHSDKLFQIIHSLVRSSKELRANFMKY 282
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 316 VGNCLDANvprgHLWSSINASLEQTahstSSDAFMTNLTAVLVRLCAP-LCMPSLKVLLVDPTYCAVPNKDrqAKGVSML 394
Cdd:COG5113 283 FAKVINVN----HERSKTIFSWREN----ISDGFMYNMSMVLSRFSRPfLDIGCSKIDMVDKIYFNNPRVD--IKEETKL 352
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 395 RAHAETclltSEEGEERLTAEKYNFVTEIFYMT---HKCFELSNIPCIERFVRVLRELQNT-----QMAYGEIVNSDPNS 466
Cdd:COG5113 353 NVDEKS----LDSFYTKPAEGSNNFISDIFFLYltkIHYGVNATFTSCEKFGEYIRKLKESleyecRLLDGSFQATRLTA 428
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 467 -----EVAKNLFRMIRDQIQQVLTIKNTLAEptndmyLLKFFEASAIWLTEIAmlpreiyeqclDKRDFSPQVFRNMELL 541
Cdd:COG5113 429 qlsrmEAYLKGIDSKMSALNGFLFMTSLFAD------EFPFTDFMTEYLARVE-----------DPWPTYPFYYKTLPWM 491
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 542 SDTP-PFvapymQSVPESIIDNIsafLNAARKLNGEQYINIYFSAHDAFFKMIILFMGSSALVKNPHLRAKLAEALEFLL 620
Cdd:COG5113 492 ENAPmTF-----KLIPEATIENA---LNYVLESIKDWRSPIFKKELEPLCEFVKIVLHRSSAIKNPMLNRKLDYYLSLGR 563
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 621 PSRIMGShrKTFVSHVFDNhpDRL---KVVRSLLNVFVSIEMTGQSVQFEQKFNYRRPMYAIMEFLWTKPEHvqcFRDLA 697
Cdd:COG5113 564 DEMRMES--RSIIHDIFKE--GKVfsrWLLPALMAFYIEIESTGQSTQFYDKFNIRFIICMMKDFEYKQPSY---SEGLS 636
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 698 VEAEQNMdaiepPIFLRFINLLINDAIFLLDESLSNLEQIKQLQQAQDNGEWESLPHTEREQHMTNLQHLGMLARFDNII 777
Cdd:COG5113 637 SIKDTNL-----PFFVKFDAKMLNDLTRLLDEALKELVEEHNIQSLLADAISNSNISERIGELQKSLAFAKRQARNSCLL 711
                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 778 GRDTINLLKLLTSKIKSIFCHNSMVDRMAAMLNYFLLNLVGPKKERFKVKDKKEFEFDPAQTVIEISHIYINLSSDESFC 857
Cdd:COG5113 712 VDGCFDLFTHILDEIPDAFLVDEIVSRLARMLNYNLKILTGPKCTDLKVKDPEQYGFNAKNLLRRMVMVYINLRSESKFV 791
                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 858 LAVSQDGRSYSEQLFSYAENILIR--IGGGQLIGDMSEFAVKVARMGAQYKEEQELLADAPEEYLDPIISTLMTDPVVLP 935
Cdd:COG5113 792 EAVASDKRSFDIDFFRRALRICENkyLISESQIEELRSFINRLEKVRVIEAVEEEDMGDVPDEFLDPLMFTIMKDPVKLP 871
                       810       820       830       840       850
                ....*....|....*....|....*....|....*....|....*....|....*
gi 19920838 936 SSKVTVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEALKQEIESWIQGKREAAR 990
Cdd:COG5113 872 TSRITIDRSTIKAHLLSDGTDPFNRMPLTLDDVTPNAELREKINRFYKCKGQKHG 926
RING-Ubox_UBE4A cd16657
U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and ...
917-986 7.60e-41

U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and similar proteins; This subfamily includes yeast ubiquitin fusion degradation protein 2 (UFD2p) and its mammalian homolog, UBE4A. Yeast UFD2p, also known as ubiquitin conjugation factor E4 or UB fusion protein 2, is a polyubiquitin chain conjugation factor (E4) in the ubiquitin fusion degradation (UFD) pathway which catalyzes elongation of the ubiquitin chain through Lys48 linkage. It binds to substrates conjugated with one to three ubiquitin molecules and catalyzes the addition of further ubiquitin moieties in the presence of ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3), yielding multiubiquitylated substrates that are targets for the 26S proteasome. UFD2p is implicated in cell survival under stress conditions and is essential for homoeostasis of unsaturated fatty acids. It interacts with UBL-UBA proteins Rad23 and Dsk2, which are involved in the endoplasmic reticulum-associated degradation, ubiquitin fusion degradation, and OLE-1 gene induction pathways. UBE4A is a U-box-type ubiquitin-protein ligase that is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. It may have a specific role in different biochemical processes other than ubiquitination, including growth or differentiation. Members of this family contain an N-terminal ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus.


Pssm-ID: 438319  Cd Length: 70  Bit Score: 144.34  E-value: 7.60e-41
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 917 EEYLDPIISTLMTDPVVLPSSKVTVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEALKQEIESWIQGKR 986
Cdd:cd16657   1 DEFLDPIMYTLMKDPVILPSSKVTVDRSTIKRHLLSDQTDPFNRSPLTLDMVIPNEELKQKIEEFLAEKK 70
RING-Ubox_UBE4B cd16658
U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 B (UBE4B) and ...
912-986 6.16e-37

U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 B (UBE4B) and similar proteins; UBE4B, also known as UFD2a, is a U-box-type ubiquitin-protein ligase that functions as an E3 ubiquitin ligase and an E4 polyubiquitin chain elongation factor, which catalyzes formation of Lys27- and Lys33-linked polyubiquitin chains rather than the Lys48-linked chain. It is a mammalian homolog of yeast UFD2 ubiquitination factor and it participates in the proteasomal degradation of misfolded or damaged proteins through association with chaperones. It is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. UBE4B has contradictory functions upon tumorigenesis as an oncogene or tumor suppressor in different types of cancers. It is essential for Hdm2 (also known as Mdm2)-mediated p53 degradation. It mediates p53 polyubiquitination and degradation, as well as inhibits p53-dependent transactivation and apoptosis, and thus plays an important role in regulating phosphorylated p53 following DNA damage. UBE4B is also associated with other pathways independent of the p53 family, such as polyglutamine aggregation and Wallerian degeneration, both of which are critical in neurodegenerative diseases. Moreover, UBE4B acts as a regulator of epidermal growth factor receptor (EGFR) degradation. It is recruited to endosomes in response to EGFR activation by binding to Hrs, a key component of endosomal sorting complex required for transport (ESCRT) 0, and then regulates endosomal sorting, affecting cellular levels of the EGFR and its downstream signaling. UBE4B contains a ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus.


Pssm-ID: 438320  Cd Length: 74  Bit Score: 133.17  E-value: 6.16e-37
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19920838 912 LADAPEEYLDPIISTLMTDPVVLPSSKVtVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEALKQEIESWIQGKR 986
Cdd:cd16658   1 LGDAPDEFLDPLMDTLMTDPVILPSGTI-MDRSIILRHLLNSQTDPFNRQPLTEDMLEPVPELKERIQAWIREKQ 74
U-box pfam04564
U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast ...
915-987 9.12e-32

U-box domain; The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues.


Pssm-ID: 398320 [Multi-domain]  Cd Length: 73  Bit Score: 118.18  E-value: 9.12e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19920838   915 APEEYLDPIISTLMTDPVVLPSSkVTVDRSTIARHLLS-DQTDPFNREPLTMDKVKSNEALKQEIESWIQGKRE 987
Cdd:pfam04564   1 IPDEFLDPITFELMTDPVILPSG-ITYDRSTIERHLLSvDPTDPFTREPLTHDQLIPNLELKAKIDAWLEEKRW 73
Ubox smart00504
Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2 ...
918-981 1.26e-19

Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.


Pssm-ID: 128780 [Multi-domain]  Cd Length: 63  Bit Score: 83.44  E-value: 1.26e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19920838    918 EYLDPIISTLMTDPVVLPSSkVTVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEALKQEIESW 981
Cdd:smart00504   1 EFLCPISLEVMKDPVILPSG-QTYERSAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQEW 63
RING-Ubox cd16453
U-box domain, a modified RING finger; The U-box protein family is a family of E3 enzymes that ...
919-963 6.00e-15

U-box domain, a modified RING finger; The U-box protein family is a family of E3 enzymes that also includes the HECT family and the RING finger family. The E3 enzyme is ubiquitin-protein ligase that cooperates with a ubiquitin-activating enzyme (E1) and a ubiquitin-conjugating enzyme (E2), and plays a central role in determining the specificity of the ubiquitination system. It removes the ubiquitin molecule from the E2 enzyme and attaches it to the target substrate, forming a covalent bond between ubiquitin and the target. U-box proteins are characterized by the presence of a U-box domain of approximately 70 amino acids. The U-box is a modified form of the RING finger domain that lacks metal chelating cysteines and histidines. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms.


Pssm-ID: 438117 [Multi-domain]  Cd Length: 44  Bit Score: 69.51  E-value: 6.00e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 19920838 919 YLDPIISTLMTDPVVLPSsKVTVDRSTIARHLLSDQTDPFNREPL 963
Cdd:cd16453   1 FLCPISGELMKDPVITPS-GITYDRSAIERWLLSDNTDPFTREPL 44
RING-Ubox_RNF37 cd16660
U-box domain, a modified RING finger, found in RING finger protein 37 (RNF37); RNF37, also ...
916-958 7.51e-11

U-box domain, a modified RING finger, found in RING finger protein 37 (RNF37); RNF37, also known as KIAA0860, U-box domain-containing protein 5 (UBOX5), UbcM4-interacting protein 5 (UIP5), or ubiquitin-conjugating enzyme 7-interacting protein 5, is an E3 ubiquitin-protein ligase found exclusively in the nucleus as part of a nuclear dot-like structure. It interacts with the molecular chaperone VCP/p97 protein. RNF37 contains a U-box domain followed by a potential nuclear location signal (NLS), and a C-terminal C3HC4-type RING-HC finger. The U-box domain is a modified RING finger domain that lacks the hallmark metal-chelating cysteines and histidines of the latter, but is likely to adopt a RING finger-like conformation. The presence of the U-box, but not of the RING finger, is required for the E3 activity. The U-box domain can directly interact with several E2 enzymes, including UbcM2, UbcM3, UbcM4, UbcH5, and UbcH8, suggesting a similar function as the RING finger in the ubiquitination pathway. This model corresponds to the U-box domain.


Pssm-ID: 438322  Cd Length: 53  Bit Score: 58.09  E-value: 7.51e-11
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 19920838 916 PEEYLDPIISTLMTDPVVLPSSKVtVDRSTIARHLLSDQT------DPF 958
Cdd:cd16660   1 PEEFLDPITCELMTLPVLLPSGKV-VDQSTLEKYIKEEATwgrlpsDPF 48
RING-Ubox_CHIP cd16654
U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein ...
915-982 1.05e-10

U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein (CHIP) and similar proteins; CHIP, also known as STIP1 homology and U box-containing protein 1 (STUB1), CLL-associated antigen KW-8, or Antigen NY-CO-7, is a multifunctional protein that functions both as a co-chaperone and an E3 ubiquitin-protein ligase. It couples protein folding and proteasome mediated degradation by interacting with heat shock proteins (e.g. HSC70) and ubiquitinating their misfolded client proteins, thereby targeting them for proteasomal degradation. It is also important for cellular differentiation and survival (or apoptosis), as well as susceptibility to stress. It targets a wide range of proteins, such as expanded ataxin-1, ataxin-3, huntingtin, and androgen receptor, which play roles in glucocorticoid response, tau degradation, and both p53 and cAMP signaling. CHIP contains an N-terminal tetratricopeptide repeat (TPR) domain responsible for protein-protein interaction, a highly charged middle coiled-coil (CC), and a C-terminal RING-like U-box domain acting as an ubiquitin ligase.


Pssm-ID: 438316 [Multi-domain]  Cd Length: 71  Bit Score: 58.36  E-value: 1.05e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19920838 915 APEEYLDPIISTLMTDPVVLPSSkVTVDRSTIARHLLSD-QTDPFNREPLTMDKVKSNEALKQEIESWI 982
Cdd:cd16654   1 VPDYLCCKISFELMRDPVITPSG-ITYERKDIEEHLQRVgHFDPITREPLTQDQLIPNLALKEAIEAFL 68
RING-Ubox_LubX-like_rpt2 cd23150
second U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein ...
916-985 6.66e-08

second U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX and similar proteins; LubX, also called RING-type E3 ubiquitin transferase LubX, is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. LubX acts as an E3 ubiquitin-protein ligase (EC 2.3.2.27) that interferes with the host's ubiquitination pathway. LubX contains two RING-like U-box domains. U-box 1 is critical to the ubiquitin ligase activity, and U-box 2 mediates interaction with host target. This model corresponds to the second one.


Pssm-ID: 438512 [Multi-domain]  Cd Length: 69  Bit Score: 50.54  E-value: 6.66e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920838 916 PEEYLDPIISTLMTDPVVLPSSKvTVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEALKQEIESWIQGK 985
Cdd:cd23150   1 PDIFLCPISKTLIKTPVITAQGK-VYDQEALSNFLIATGNKDETGKKLSIDDVVVFDELYQQIKVYNFYR 69
RING-Ubox_LubX-like_rpt1 cd23149
first U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX ...
919-974 3.87e-07

first U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX and similar proteins; LubX, also called RING-type E3 ubiquitin transferase LubX, is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. LubX acts as an E3 ubiquitin-protein ligase (EC 2.3.2.27) that interferes with the host's ubiquitination pathway. LubX contains two RING-like U-box domains. U-box 1 is critical to the ubiquitin ligase activity, and U-box 2 mediates interaction with host target. This model corresponds to the first one.


Pssm-ID: 438511 [Multi-domain]  Cd Length: 55  Bit Score: 47.86  E-value: 3.87e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19920838 919 YLDPIISTLMTDPVVLPSSKvTVDRSTIARHLLSDQTDPFNREPLTMDKVKSNEAL 974
Cdd:cd23149   1 FTCPITSGFMEDPVITPSGF-SYERSAIERWLETKPEDPQTREPLTAKDLQPNREL 55
RING-Ubox_WDSUB1-like cd16655
U-box domain, a modified RING finger, found in WD repeat, SAM and U-box domain-containing ...
916-971 1.56e-06

U-box domain, a modified RING finger, found in WD repeat, SAM and U-box domain-containing protein 1 (WDSUB1) and similar proteins; WDSUB1 is an uncharacterized protein containing seven WD40 repeats and a SAM domain in addition to the U-box. Its biological role remains unclear. This subfamily also includes many uncharacterized kinase domain-containing U-box (AtPUB) proteins and several MIF4G motif-containing AtPUB proteins from Arabidopsis.


Pssm-ID: 438317 [Multi-domain]  Cd Length: 55  Bit Score: 45.96  E-value: 1.56e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19920838 916 PEEYLDPIISTLMTDPVVLPSSkVTVDRSTIARHLLSDQTDPFNREPLTMDKVKSN 971
Cdd:cd16655   1 PDEFLCPITQELMRDPVVAADG-HTYERSAIEEWLETHNTSPMTRLPLSSTDLVPN 55
RING_Ubox cd00162
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
921-959 4.94e-06

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438111 [Multi-domain]  Cd Length: 42  Bit Score: 44.37  E-value: 4.94e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 19920838 921 DPIISTLMTD--PVVLPSSKVTVDRSTIARHLLS-DQTDPFN 959
Cdd:cd00162   1 CPICREEMNDrrPVVLLSCGHTFSRSAIARWLEGsKQKCPFC 42
RING-Ubox_PUB cd16664
U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and ...
916-964 3.84e-04

U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and similar proteins; The plant PUB proteins, also known as U-box domain-containing proteins, are much more numerous in Arabidopsis which has 62 in comparison with the typical 6 in most animals. The majority of AtPUBs in this subfamily are known as ARM domain-containing PUB proteins, containing a C-terminally-located, tandem ARM (armadillo) repeat protein-interaction region in addition to the U-box domain. They have been implicated in the regulation of cell death and defense. They also play important roles in other plant-specific pathways, such as controlling both self-incompatibility and pseudo-self-incompatibility, as well as acting in abiotic stress. A subgroup of ARM domain-containing PUB proteins harbors a plant-specific U-box N-terminal domain.


Pssm-ID: 438326 [Multi-domain]  Cd Length: 53  Bit Score: 39.08  E-value: 3.84e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 19920838 916 PEEYLDPIISTLMTDPVVLPSSkVTVDRSTIARHLLS-DQTDPFNREPLT 964
Cdd:cd16664   1 PEEFICPISLELMKDPVILATG-QTYERAAIEKWLDSgNNTCPITGQPLT 49
RING-Ubox_PRP19 cd16656
U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and ...
930-966 8.51e-03

U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and similar proteins; Prp19, also known as nuclear matrix protein 200 (NMP200), senescence evasion factor (SNEV), or DNA repair protein Pso4 (psoralen-sensitive mutant 4), is a ubiquitously expressed multifunctional E3 ubiquitin ligase with pleiotropic activities in DNA damage signaling, repair, and replicative senescence. It functions as a critical component of DNA repair and DNA damage checkpoint complexes. It senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, and regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex. Prp19 contains an N-terminal E3 ubiquitin ligase U-box domain with E2 recruitment function that facilitates dimerization and is essential for its auto-ubiquitination activity in vitro or when overexpressed, a coiled-coil Prp19 homology region that mediates its tetramerization and interaction with CDC5L and SPF27, and a C-terminal seven-bladed WD40 beta-propeller type of leucine-rich architectural repeats that form an asymmetrical barrel-shaped structure important for substrate recognition and recruitment.


Pssm-ID: 438318  Cd Length: 54  Bit Score: 35.62  E-value: 8.51e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 19920838 930 DPVVLPSSKVTVDRSTIARHLLSDQTDPFNREPLTMD 966
Cdd:cd16656  12 EPVVSPKSGHVFEKRLIEKYIAENGTDPVTGEPLTEE 48
 
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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