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Degradation in the endoplasmic reticulum protein 1

 DER1_YEAST              Reviewed;         211 AA.
P38307; D6VQJ8;
01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
05-OCT-2010, sequence version 3.
25-MAY-2022, entry version 161.
RecName: Full=Degradation in the endoplasmic reticulum protein 1;
Name=DER1; OrderedLocusNames=YBR201W; ORFNames=YBR1413;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=8631297; DOI=10.1002/j.1460-2075.1996.tb00411.x;
Knop M., Finger A., Braun T., Hellmuth K., Wolf D.H.;
"Der1, a novel protein specifically required for endoplasmic reticulum
degradation in yeast.";
EMBO J. 15:753-763(1996).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7975899; DOI=10.1002/yea.320100612;
Mallet L., Bussereau F., Jacquet M.;
"Nucleotide sequence analysis of an 11.7 kb fragment of yeast chromosome II
including BEM1, a new gene of the WD-40 repeat family and a new member of
the KRE2/MNT1 family.";
Yeast 10:819-831(1994).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
Mewes H.-W., Kleine K.;
"Complete DNA sequence of yeast chromosome II.";
EMBO J. 13:5795-5809(1994).
[4]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
G3 (Bethesda) 4:389-398(2014).
[5]
INDUCTION.
PubMed=10847680; DOI=10.1016/s0092-8674(00)80835-1;
Travers K.J., Patil C.K., Wodicka L., Lockhart D.J., Weissman J.S.,
Walter P.;
"Functional and genomic analyses reveal an essential coordination between
the unfolded protein response and ER-associated degradation.";
Cell 101:249-258(2000).
[6]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[7]
MEMBRANE TOPOLOGY, AND MUTANT DER1-2.
PubMed=15093775; DOI=10.1016/j.femsyr.2004.02.003;
Hitt R., Wolf D.H.;
"Der1p, a protein required for degradation of malfolded soluble proteins of
the endoplasmic reticulum: topology and Der1-like proteins.";
FEMS Yeast Res. 4:721-729(2004).
[8]
FUNCTION, IDENTIFICATION IN THE HRD1 COMPLEX, AND DISRUPTION PHENOTYPE.
PubMed=16873066; DOI=10.1016/j.cell.2006.05.043;
Carvalho P., Goder V., Rapoport T.A.;
"Distinct ubiquitin-ligase complexes define convergent pathways for the
degradation of ER proteins.";
Cell 126:361-373(2006).
[9]
TOPOLOGY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 208353 / W303-1A;
PubMed=16847258; DOI=10.1073/pnas.0604075103;
Kim H., Melen K., Oesterberg M., von Heijne G.;
"A global topology map of the Saccharomyces cerevisiae membrane proteome.";
Proc. Natl. Acad. Sci. U.S.A. 103:11142-11147(2006).
[10]
FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH USA1.
PubMed=20005842; DOI=10.1016/j.molcel.2009.10.015;
Horn S.C., Hanna J., Hirsch C., Volkwein C., Schutz A., Heinemann U.,
Sommer T., Jarosch E.;
"Usa1 functions as a scaffold of the HRD-ubiquitin ligase.";
Mol. Cell 36:782-793(2009).
[11]
FUNCTION, DISRUPTION PHENOTYPE, ACETYLATION AT MET-1, AND MUTAGENESIS OF
ASP-2.
PubMed=23363603; DOI=10.1091/mbc.e12-11-0838;
Zattas D., Adle D.J., Rubenstein E.M., Hochstrasser M.;
"N-terminal acetylation of the yeast Derlin Der1 is essential for Hrd1
ubiquitin-ligase activity toward luminal ER substrates.";
Mol. Biol. Cell 24:890-900(2013).
[12] {ECO:0007744|PDB:6VJZ, ECO:0007744|PDB:6VK0}
STRUCTURE BY ELECTRON MICROSCOPY (4.10 ANGSTROMS) IN COMPLEX WITH HRD1;
HRD3 AND USA1, FUNCTION, SUBUNIT, INTERACTION WITH USA1, TRANSMEMBRANE
DOMAINS, AND MUTAGENESIS OF 79-ASN--THR-83.
PubMed=32327568; DOI=10.1126/science.aaz2449;
Wu X., Siggel M., Ovchinnikov S., Mi W., Svetlov V., Nudler E., Liao M.,
Hummer G., Rapoport T.A.;
"Structural basis of ER-associated protein degradation mediated by the Hrd1
ubiquitin ligase complex.";
Science 368:0-0(2020).
-!- FUNCTION: Component of the endoplasmic reticulum-associated degradation
(ERAD) pathway. Specifically required for the ERAD-L pathway which
mediates the degradation of proteins with misfolded lumenal domains
within the endoplasmic reticulum (ER). Facilitates retrotranslocation
of misfolded proteins from the ER lumen through the ER membrane in
conjunction with HRD1 (PubMed:32327568). Both proteins have lateral
gates facing each other and distort the membrane region between the
lateral gates, making it much thinner than a normal phospholipid
bilayer (PubMed:32327568). Substrates insert into the membrane as a
hairpin loop with one strand interacting with DER1 and the other with
HRD1 (PubMed:32327568). {ECO:0000269|PubMed:16873066,
ECO:0000269|PubMed:20005842, ECO:0000269|PubMed:23363603,
ECO:0000269|PubMed:32327568, ECO:0000269|PubMed:8631297}.
-!- SUBUNIT: Component of the HRD1 ubiquitin ligase complex which contains
the E3 ligase HRD1, its cofactors HRD3, USA1 and DER1, substrate
recruiting factor YOS9 and CDC48-binding protein UBX2 (PubMed:16873066,
PubMed:32327568). Within the complex, interacts with USA1 (via C-
terminus) (PubMed:20005842, PubMed:32327568). In ERAD-L, HRD3 and YOS9
jointly bind misfolded glycoproteins in the endoplasmic reticulum (ER)
lumen (PubMed:32327568). Movement of ERAD-L substrates through the ER
membrane is facilitated by HRD1 and DER1 which have lateral gates
facing each other and which distort the membrane region between the
lateral gates, making it much thinner than a normal phospholipid
bilayer (PubMed:32327568). Substrates insert into the membrane as a
hairpin loop with one strand interacting with DER1 and the other with
HRD1 (PubMed:32327568). The HRD1 complex interacts with the
heterotrimeric CDC48-NPL4-UFD1 ATPase complex which is recruited by
UBX2 via its interaction with CDC48 and which moves ubiquitinated
substrates to the cytosol for targeting to the proteasome
(PubMed:16873066). {ECO:0000269|PubMed:16873066,
ECO:0000269|PubMed:20005842, ECO:0000269|PubMed:32327568}.
-!- INTERACTION:
P38307; P25694: CDC48; NbExp=5; IntAct=EBI-5761, EBI-4308;
P38307; Q08109: HRD1; NbExp=5; IntAct=EBI-5761, EBI-37613;
P38307; Q05787: HRD3; NbExp=3; IntAct=EBI-5761, EBI-31647;
P38307; P00729: PRC1; NbExp=2; IntAct=EBI-5761, EBI-4153;
P38307; P53044: UFD1; NbExp=3; IntAct=EBI-5761, EBI-19997;
P38307; Q03714: USA1; NbExp=3; IntAct=EBI-5761, EBI-27760;
-!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
{ECO:0000269|PubMed:8631297}; Multi-pass membrane protein
{ECO:0000269|PubMed:8631297}.
-!- INDUCTION: Up-regulated by the unfolded protein response (UPR).
{ECO:0000269|PubMed:10847680}.
-!- PTM: N-terminally acetylated by acetyltransferase NatB which enhances
DER1 stability and is required for ERAD-L function.
{ECO:0000269|PubMed:23363603}.
-!- DISRUPTION PHENOTYPE: Impaired degradation of proteins with misfolded
lumenal domains such as CPY*, a mutant, misfolded form of
carboxypeptidase Y which is a known ERAD-L substrate. Degradation of
proteins with misfolded intramembrane domains is not affected.
{ECO:0000269|PubMed:16873066, ECO:0000269|PubMed:20005842,
ECO:0000269|PubMed:23363603}.
-!- MISCELLANEOUS: Present with 238 molecules/cell in log phase SD medium.
{ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the derlin family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAA79688.1; Type=Frameshift; Evidence={ECO:0000305};
---------------------------------------------------------------------------
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EMBL; X92435; CAA63165.1; -; Genomic_DNA.
EMBL; Z21487; CAA79688.1; ALT_FRAME; Genomic_DNA.
EMBL; Z36069; CAA85164.1; -; Genomic_DNA.
EMBL; Z36070; CAA85165.1; -; Genomic_DNA.
EMBL; BK006936; DAA07318.1; -; Genomic_DNA.
PIR; S45450; S45450.
RefSeq; NP_009760.1; NM_001178549.1.
PDB; 6VJZ; EM; 4.30 A; C=1-211.
PDB; 6VK0; EM; 4.10 A; C=1-211.
PDBsum; 6VJZ; -.
PDBsum; 6VK0; -.
AlphaFoldDB; P38307; -.
SMR; P38307; -.
BioGRID; 32898; 252.
ComplexPortal; CPX-3070; HRD1 ubiquitin ligase complex.
DIP; DIP-4767N; -.
IntAct; P38307; 9.
MINT; P38307; -.
STRING; 4932.YBR201W; -.
TCDB; 3.A.16.1.2; the endoplasmic reticular retrotranslocon (er-rt) family.
iPTMnet; P38307; -.
MaxQB; P38307; -.
PaxDb; P38307; -.
PRIDE; P38307; -.
EnsemblFungi; YBR201W_mRNA; YBR201W; YBR201W.
GeneID; 852500; -.
KEGG; sce:YBR201W; -.
SGD; S000000405; DER1.
VEuPathDB; FungiDB:YBR201W; -.
eggNOG; KOG0858; Eukaryota.
HOGENOM; CLU_1256224_0_0_1; -.
InParanoid; P38307; -.
OMA; KKGQYER; -.
Reactome; R-SCE-5358346; Hedgehog ligand biogenesis.
PRO; PR:P38307; -.
Proteomes; UP000002311; Chromosome II.
RNAct; P38307; protein.
GO; GO:0005789; C:endoplasmic reticulum membrane; IDA:SGD.
GO; GO:0000836; C:Hrd1p ubiquitin ligase complex; IPI:ComplexPortal.
GO; GO:0000839; C:Hrd1p ubiquitin ligase ERAD-L complex; IDA:SGD.
GO; GO:0030176; C:integral component of endoplasmic reticulum membrane; IBA:GO_Central.
GO; GO:0051787; F:misfolded protein binding; IDA:SGD.
GO; GO:1990381; F:ubiquitin-specific protease binding; IBA:GO_Central.
GO; GO:0030968; P:endoplasmic reticulum unfolded protein response; IBA:GO_Central.
GO; GO:0070843; P:misfolded protein transport; IMP:SGD.
GO; GO:0006515; P:protein quality control for misfolded or incompletely synthesized proteins; IMP:UniProtKB.
GO; GO:0030970; P:retrograde protein transport, ER to cytosol; IMP:SGD.
GO; GO:0030433; P:ubiquitin-dependent ERAD pathway; IMP:SGD.
InterPro; IPR007599; DER1.
Pfam; PF04511; DER1; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Endoplasmic reticulum; Membrane;
Protein transport; Reference proteome; Transmembrane; Transmembrane helix;
Transport.
CHAIN 1..211
/note="Degradation in the endoplasmic reticulum protein 1"
/id="PRO_0000219053"
TOPO_DOM 1..14
/note="Cytoplasmic"
/evidence="ECO:0000269|PubMed:32327568"
TRANSMEM 15..32
/note="Helical; Name=1"
/evidence="ECO:0000269|PubMed:32327568"
TOPO_DOM 33..67
/note="Lumenal"
/evidence="ECO:0000269|PubMed:32327568"
TRANSMEM 68..85
/note="Helical; Name=2"
/evidence="ECO:0000269|PubMed:32327568"
TOPO_DOM 86..92
/note="Cytoplasmic"
/evidence="ECO:0000269|PubMed:32327568"
TRANSMEM 93..109
/note="Helical; Name=3"
/evidence="ECO:0000269|PubMed:32327568"
TOPO_DOM 110..117
/note="Lumenal"
/evidence="ECO:0000269|PubMed:32327568"
TRANSMEM 118..133
/note="Helical; Name=4"
/evidence="ECO:0000269|PubMed:32327568"
TOPO_DOM 134..149
/note="Cytoplasmic"
/evidence="ECO:0000269|PubMed:32327568"
TRANSMEM 150..165
/note="Helical; Name=5"
/evidence="ECO:0000269|PubMed:32327568"
TOPO_DOM 166..168
/note="Lumenal"
/evidence="ECO:0000269|PubMed:32327568"
TRANSMEM 169..189
/note="Helical; Name=6"
/evidence="ECO:0000269|PubMed:32327568"
TOPO_DOM 190..211
/note="Cytoplasmic"
/evidence="ECO:0000269|PubMed:32327568"
MOD_RES 1
/note="N-acetylmethionine"
/evidence="ECO:0000269|PubMed:23363603"
MUTAGEN 2
/note="D->A: Cleavage of initiator methionine, acetylation
of Ala-2 by NatA, slightly reduced acetylation levels but
no significant effect on endogenous stability or ability to
degrade CPY*."
/evidence="ECO:0000269|PubMed:23363603"
MUTAGEN 2
/note="D->E: No effect on ability to degrade CPY*."
/evidence="ECO:0000269|PubMed:23363603"
MUTAGEN 2
/note="D->K: N-terminus not predicted to be acetylated.
Strongly decreases endogenous stability."
/evidence="ECO:0000269|PubMed:23363603"
MUTAGEN 2
/note="D->L: Predicted to lead to acetylation by NatC. No
effect on endogenous stability or ability to degrade CPY*."
/evidence="ECO:0000269|PubMed:23363603"
MUTAGEN 59
/note="S->L: In der1-2; impairs the ability to degrade
misfolded proteins."
MUTAGEN 79..83
/note="NHLST->LHLLV: Reduced ERAD-L degradation rate."
/evidence="ECO:0000269|PubMed:32327568"
MUTAGEN 79..83
/note="NHLST->SHLKN: No effect on ERAD-L degradation rate."
/evidence="ECO:0000269|PubMed:32327568"
CONFLICT 145
/note="A -> V (in Ref. 1; CAA63165)"
/evidence="ECO:0000305"
SEQUENCE 211 AA; 24391 MW; 41510999E92C691D CRC64;
MDAVILNLLG DIPLVTRLWT IGCLVLSGLT SLRIVDPGKV VYSYDLVFKK GQYGRLLYSI
FDYGAFNWIS MINIFVSANH LSTLENSFNL RRKFCWIIFL LLVILVKMTS IEQPAASLGV
LLHENLVYYE LKKNGNQMNV RFFGAIDVSP SIFPIYMNAV MYFVYKRSWL EIAMNFMPGH
VIYYMDDIIG KIYGIDLCKS PYDWFRNTET P


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