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1fxt

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STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX

Structural highlights

1fxt is a 2 chain structure with sequence from Homo sapiens and Saccharomyces cerevisiae. The December 2004 RCSB PDB Molecule of the Month feature on Ubiquitin by David S. Goodsell is 10.2210/rcsb_pdb/mom_2004_12. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBC1_YEAST Catalyzes the covalent attachment of ubiquitin to other proteins. Functions in degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. Cognate E2 conjugating enzyme for the HRD1 ubiquitin ligase complex, which is part of the ERAD-L and ERAD-M pathways responsible for the rapid degradation of soluble lumenal and membrane proteins with misfolded lumenal domains (ERAD-L), or ER-membrane proteins with misfolded transmembrane domains (ERAD-M).^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

BACKGROUND: Ubiquitin-conjugating enzymes (E2s) are central enzymes involved in ubiquitin-mediated protein degradation. During this process, ubiquitin (Ub) and the E2 protein form an unstable E2-Ub thiolester intermediate prior to the transfer of ubiquitin to an E3-ligase protein and the labeling of a substrate for degradation. A series of complex interactions occur among the target substrate, ubiquitin, E2, and E3 in order to efficiently facilitate the transfer of the ubiquitin molecule. However, due to the inherent instability of the E2-Ub thiolester, the structural details of this complex intermediate are not known. RESULTS: A three-dimensional model of the E2-Ub thiolester intermediate has been determined for the catalytic domain of the E2 protein Ubc1 (Ubc1(Delta450)) and ubiquitin from S. cerevisiae. The interface of the E2-Ub intermediate was determined by kinetically monitoring thiolester formation by 1H-(15)N HSQC spectra by using combinations of 15N-labeled and unlabeled Ubc1(Delta450) and Ub proteins. By using the surface interface as a guide and the X-ray structures of Ub and the 1.9 A structure of Ubc1(Delta450) determined here, docking simulations followed by energy minimization were used to produce the first model of a E2-Ub thiolester intermediate. CONCLUSIONS: Complementary surfaces were found on the E2 and Ub proteins whereby the C terminus of Ub wraps around the E2 protein terminating in the thiolester between C88 (Ubc1(Delta450)) and G76 (Ub). The model supports in vivo and in vitro experiments of E2 derivatives carrying surface residue substitutions. Furthermore, the model provides insights into the arrangement of Ub, E2, and E3 within a ternary targeting complex.

Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail.,Hamilton KS, Ellison MJ, Barber KR, Williams RS, Huzil JT, McKenna S, Ptak C, Glover M, Shaw GS Structure. 2001 Oct;9(10):897-904. PMID:11591345^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Friedlander R, Jarosch E, Urban J, Volkwein C, Sommer T. A regulatory link between ER-associated protein degradation and the unfolded-protein response. Nat Cell Biol. 2000 Jul;2(7):379-84. PMID:10878801 doi:http://dx.doi.org/10.1038/35017001
↑ Bays NW, Gardner RG, Seelig LP, Joazeiro CA, Hampton RY. Hrd1p/Der3p is a membrane-anchored ubiquitin ligase required for ER-associated degradation. Nat Cell Biol. 2001 Jan;3(1):24-9. PMID:11146622 doi:10.1038/35050524
↑ Hamilton KS, Ellison MJ, Barber KR, Williams RS, Huzil JT, McKenna S, Ptak C, Glover M, Shaw GS. Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail. Structure. 2001 Oct;9(10):897-904. PMID:11591345

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1fxt"

@@ Line 1: / Line 1: @@
 ==STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX==
-<StructureSection load='1fxt' size='340' side='right'caption='[[1fxt]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
+<StructureSection load='1fxt' size='340' side='right'caption='[[1fxt]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1fxt]] is a 2 chain structure. The December 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Ubiquitin''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_12 10.2210/rcsb_pdb/mom_2004_12]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FXT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1fxt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. The December 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Ubiquitin''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_12 10.2210/rcsb_pdb/mom_2004_12]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FXT FirstGlance]. <br>
-</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fxt OCA], [https://pdbe.org/1fxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fxt RCSB], [https://www.ebi.ac.uk/pdbsum/1fxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fxt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/UBC1_YEAST UBC1_YEAST]] Catalyzes the covalent attachment of ubiquitin to other proteins. Functions in degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. Cognate E2 conjugating enzyme for the HRD1 ubiquitin ligase complex, which is part of the ERAD-L and ERAD-M pathways responsible for the rapid degradation of soluble lumenal and membrane proteins with misfolded lumenal domains (ERAD-L), or ER-membrane proteins with misfolded transmembrane domains (ERAD-M).<ref>PMID:10878801</ref> <ref>PMID:11146622</ref>
+[https://www.uniprot.org/uniprot/UBC1_YEAST UBC1_YEAST] Catalyzes the covalent attachment of ubiquitin to other proteins. Functions in degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. Cognate E2 conjugating enzyme for the HRD1 ubiquitin ligase complex, which is part of the ERAD-L and ERAD-M pathways responsible for the rapid degradation of soluble lumenal and membrane proteins with misfolded lumenal domains (ERAD-L), or ER-membrane proteins with misfolded transmembrane domains (ERAD-M).<ref>PMID:10878801</ref> <ref>PMID:11146622</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
+[[Category: Saccharomyces cerevisiae]]
 [[Category: Ubiquitin]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Ellison MJ]]
-[[Category: Ellison, M J]]
+[[Category: Glover M]]
-[[Category: Glover, M]]
+[[Category: Hamilton KS]]
-[[Category: Hamilton, K S]]
+[[Category: Huzil JT]]
-[[Category: Huzil, J T]]
+[[Category: McKenna S]]
-[[Category: McKenna, S]]
+[[Category: Ptak C]]
-[[Category: Ptak, C]]
+[[Category: Shaw GS]]
-[[Category: Shaw, G S]]
+[[Category: Williams RS]]
-[[Category: Williams, R S]]
-[[Category: Ligase]]
-[[Category: Model of the interaction between yeast ubc1 and ubiquitin after the formation of a covalent thiolester]]

1fxt

From Proteopedia

Current revision

STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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