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| - | [[Image:2ucz.gif|left|200px]]<br /><applet load="2ucz" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="2ucz, resolution 2.93Å" /> | |
| - | '''UBIQUITIN CONJUGATING ENZYME (UBC7) FROM SACCHAROMYCES CEREVISIAE'''<br /> | |
| | | | |
| - | ==Overview== | + | ==UBIQUITIN CONJUGATING ENZYME (UBC7) FROM SACCHAROMYCES CEREVISIAE== |
| - | Ubiquitin-conjugating enzymes are a family of related proteins that, participate in the ubiquitination of proteins. Previous studies on the, crystal structures of Saccharomyces cerevisiae Ubc4 and Arabidopsis, thaliana Ubc1 indicated that the smallest enzymes (class I), which consist, entirely of the conserved core domain, share a common tertiary fold. Here, we report the three-dimensional structure of the S. cerevisiae class I, enzyme encoded by the UBC7 gene. The crystal structure has been solved, using molecular replacement techniques and refined by simulated annealing, to an R-factor of 0.183 at 2.93 A resolution. Bond lengths and angles in, the molecule have root-mean-square deviations from ideal values of 0.016 A, and 2.3 degrees, respectively. Ubc7 is an alpha/beta protein with four, alpha-helices and a four-stranded antiparallel beta-sheet. With the, exception of two regions where extra residues are present, the tertiary, folding of Ubc7 is similar to those of the other two enzymes. The, ubiquitin-accepting cysteine is located in a cleft between two loops. One, of these loops is nonconserved, as this region of the Ubc7 molecule, differs from the other two enzymes by having 13 extra residues. There is, also a second single amino acid insertion that alters the orientation of, the turn between the first two beta-strands. Analysis of the 13, ubiquitin-conjugating enzyme sequences in S. cerevisiae indicates that, there may be two other regions where extra residues could be inserted into, the common tertiary fold. Both of these other regions exhibit significant, deviations in the superposition of the three structures and, like the two, insertion regions in Ubc7, may represent hypervariable regions within a, common tertiary fold. As ubiquitin-conjugating enzymes interact with, different substrates or other accessory proteins in the ubiquitination, pathway, these variable surface regions may confer distinct specificity to, individual enzymes. | + | <StructureSection load='2ucz' size='340' side='right'caption='[[2ucz]], [[Resolution|resolution]] 2.93Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[2ucz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ucz 1ucz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UCZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UCZ FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.93Å</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=2ucz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ucz OCA], [https://pdbe.org/2ucz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ucz RCSB], [https://www.ebi.ac.uk/pdbsum/2ucz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ucz ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/UBC7_YEAST UBC7_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 DOA10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains, and of 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). Involved in resistance to cadmium poisoning.<ref>PMID:8393731</ref> <ref>PMID:9388185</ref> <ref>PMID:9695950</ref> <ref>PMID:11641273</ref> <ref>PMID:11390656</ref> <ref>PMID:11146622</ref> <ref>PMID:16873066</ref> |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uc/2ucz_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ucz ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Ubiquitin-conjugating enzymes are a family of related proteins that participate in the ubiquitination of proteins. Previous studies on the crystal structures of Saccharomyces cerevisiae Ubc4 and Arabidopsis thaliana Ubc1 indicated that the smallest enzymes (class I), which consist entirely of the conserved core domain, share a common tertiary fold. Here we report the three-dimensional structure of the S. cerevisiae class I enzyme encoded by the UBC7 gene. The crystal structure has been solved using molecular replacement techniques and refined by simulated annealing to an R-factor of 0.183 at 2.93 A resolution. Bond lengths and angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 2.3 degrees, respectively. Ubc7 is an alpha/beta protein with four alpha-helices and a four-stranded antiparallel beta-sheet. With the exception of two regions where extra residues are present, the tertiary folding of Ubc7 is similar to those of the other two enzymes. The ubiquitin-accepting cysteine is located in a cleft between two loops. One of these loops is nonconserved, as this region of the Ubc7 molecule differs from the other two enzymes by having 13 extra residues. There is also a second single amino acid insertion that alters the orientation of the turn between the first two beta-strands. Analysis of the 13 ubiquitin-conjugating enzyme sequences in S. cerevisiae indicates that there may be two other regions where extra residues could be inserted into the common tertiary fold. Both of these other regions exhibit significant deviations in the superposition of the three structures and, like the two insertion regions in Ubc7, may represent hypervariable regions within a common tertiary fold. As ubiquitin-conjugating enzymes interact with different substrates or other accessory proteins in the ubiquitination pathway, these variable surface regions may confer distinct specificity to individual enzymes. |
| | | | |
| - | ==About this Structure==
| + | Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution.,Cook WJ, Martin PD, Edwards BF, Yamazaki RK, Chau V Biochemistry. 1997 Feb 18;36(7):1621-7. PMID:9048545<ref>PMID:9048545</ref> |
| - | 2UCZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure superseeds the now removed PDB entry 1UCZ. Active as [http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] Known structural/functional Site: <scene name='pdbsite=C89:Ubiquitin-Accepting+Residue'>C89</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UCZ OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution., Cook WJ, Martin PD, Edwards BF, Yamazaki RK, Chau V, Biochemistry. 1997 Feb 18;36(7):1621-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9048545 9048545]
| + | </div> |
| - | [[Category: Saccharomyces cerevisiae]]
| + | <div class="pdbe-citations 2ucz" style="background-color:#fffaf0;"></div> |
| - | [[Category: Single protein]]
| + | |
| - | [[Category: Ubiquitin--protein ligase]]
| + | |
| - | [[Category: Chau, V.]]
| + | |
| - | [[Category: Cook, W.J.]]
| + | |
| - | [[Category: ligase]]
| + | |
| - | [[Category: ubiquitin conjugation]]
| + | |
| - | [[Category: yeast]]
| + | |
| | | | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:47:00 2008''
| + | ==See Also== |
| | + | *[[3D structures of ubiquitin conjugating enzyme|3D structures of ubiquitin conjugating enzyme]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | + | [[Category: Saccharomyces cerevisiae]] |
| | + | [[Category: Chau V]] |
| | + | [[Category: Cook WJ]] |
| Structural highlights
Function
UBC7_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 DOA10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains, and of 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). Involved in resistance to cadmium poisoning.[1] [2] [3] [4] [5] [6] [7]
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
Ubiquitin-conjugating enzymes are a family of related proteins that participate in the ubiquitination of proteins. Previous studies on the crystal structures of Saccharomyces cerevisiae Ubc4 and Arabidopsis thaliana Ubc1 indicated that the smallest enzymes (class I), which consist entirely of the conserved core domain, share a common tertiary fold. Here we report the three-dimensional structure of the S. cerevisiae class I enzyme encoded by the UBC7 gene. The crystal structure has been solved using molecular replacement techniques and refined by simulated annealing to an R-factor of 0.183 at 2.93 A resolution. Bond lengths and angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 2.3 degrees, respectively. Ubc7 is an alpha/beta protein with four alpha-helices and a four-stranded antiparallel beta-sheet. With the exception of two regions where extra residues are present, the tertiary folding of Ubc7 is similar to those of the other two enzymes. The ubiquitin-accepting cysteine is located in a cleft between two loops. One of these loops is nonconserved, as this region of the Ubc7 molecule differs from the other two enzymes by having 13 extra residues. There is also a second single amino acid insertion that alters the orientation of the turn between the first two beta-strands. Analysis of the 13 ubiquitin-conjugating enzyme sequences in S. cerevisiae indicates that there may be two other regions where extra residues could be inserted into the common tertiary fold. Both of these other regions exhibit significant deviations in the superposition of the three structures and, like the two insertion regions in Ubc7, may represent hypervariable regions within a common tertiary fold. As ubiquitin-conjugating enzymes interact with different substrates or other accessory proteins in the ubiquitination pathway, these variable surface regions may confer distinct specificity to individual enzymes.
Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution.,Cook WJ, Martin PD, Edwards BF, Yamazaki RK, Chau V Biochemistry. 1997 Feb 18;36(7):1621-7. PMID:9048545[8]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Chen P, Johnson P, Sommer T, Jentsch S, Hochstrasser M. Multiple ubiquitin-conjugating enzymes participate in the in vivo degradation of the yeast MAT alpha 2 repressor. Cell. 1993 Jul 30;74(2):357-69. PMID:8393731
- ↑ Biederer T, Volkwein C, Sommer T. Role of Cue1p in ubiquitination and degradation at the ER surface. Science. 1997 Dec 5;278(5344):1806-9. PMID:9388185
- ↑ Johnson PR, Swanson R, Rakhilina L, Hochstrasser M. Degradation signal masking by heterodimerization of MATalpha2 and MATa1 blocks their mutual destruction by the ubiquitin-proteasome pathway. Cell. 1998 Jul 24;94(2):217-27. PMID:9695950
- ↑ Swanson R, Locher M, Hochstrasser M. A conserved ubiquitin ligase of the nuclear envelope/endoplasmic reticulum that functions in both ER-associated and Matalpha2 repressor degradation. Genes Dev. 2001 Oct 15;15(20):2660-74. PMID:11641273 doi:10.1101/gad.933301
- ↑ Gardner RG, Shearer AG, Hampton RY. In vivo action of the HRD ubiquitin ligase complex: mechanisms of endoplasmic reticulum quality control and sterol regulation. Mol Cell Biol. 2001 Jul;21(13):4276-91. PMID:11390656 doi:10.1128/MCB.21.13.4276-4291.2001
- ↑ 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
- ↑ Carvalho P, Goder V, Rapoport TA. Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins. Cell. 2006 Jul 28;126(2):361-73. PMID:16873066 doi:10.1016/j.cell.2006.05.043
- ↑ Cook WJ, Martin PD, Edwards BF, Yamazaki RK, Chau V. Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution. Biochemistry. 1997 Feb 18;36(7):1621-7. PMID:9048545 doi:10.1021/bi962639e
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