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| | ==Human Ubiquitin-activating Enzyme 5 in Complex with ATP== | | ==Human Ubiquitin-activating Enzyme 5 in Complex with ATP== |
| - | <StructureSection load='3h8v' size='340' side='right' caption='[[3h8v]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='3h8v' size='340' side='right'caption='[[3h8v]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3h8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3H8V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3h8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H8V FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3guc|3guc]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBA5, UBE1DC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3h8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h8v OCA], [https://pdbe.org/3h8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h8v RCSB], [https://www.ebi.ac.uk/pdbsum/3h8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h8v ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3h8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h8v OCA], [http://pdbe.org/3h8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3h8v RCSB], [http://www.ebi.ac.uk/pdbsum/3h8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3h8v ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/UBA5_HUMAN UBA5_HUMAN]] E1-like enzyme which activates UFM1 and SUMO2.<ref>PMID:15071506</ref> <ref>PMID:18442052</ref> <ref>PMID:20368332</ref> | + | [https://www.uniprot.org/uniprot/UBA5_HUMAN UBA5_HUMAN] E1-like enzyme which activates UFM1 and SUMO2.<ref>PMID:15071506</ref> <ref>PMID:18442052</ref> <ref>PMID:20368332</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Ubiquitin activating enzyme|Ubiquitin activating enzyme]] | + | *[[3D structures of Ubiquitin activating enzyme|3D structures of Ubiquitin activating enzyme]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Arrowsmith, C H]] | + | [[Category: Large Structures]] |
| - | [[Category: Bacik, J P]] | + | [[Category: Arrowsmith CH]] |
| - | [[Category: Bochkarev, A]] | + | [[Category: Bacik JP]] |
| - | [[Category: Bountra, C]] | + | [[Category: Bochkarev A]] |
| - | [[Category: Dhe-Paganon, S]] | + | [[Category: Bountra C]] |
| - | [[Category: Edwards, A M]] | + | [[Category: Dhe-Paganon S]] |
| - | [[Category: Rastgoo, N]] | + | [[Category: Edwards AM]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Rastgoo N]] |
| - | [[Category: Walker, J R]] | + | [[Category: Walker JR]] |
| - | [[Category: Weigelt, J]] | + | [[Category: Weigelt J]] |
| - | [[Category: Atp-binding]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Sgc]]
| + | |
| - | [[Category: Transferase]]
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| - | [[Category: Ubl conjugation pathway]]
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| Structural highlights
Function
UBA5_HUMAN E1-like enzyme which activates UFM1 and SUMO2.[1] [2] [3]
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
E1 ubiquitin-activating enzymes (UBAs) are large multidomain proteins that catalyze formation of a thioester bond between the terminal carboxylate of a ubiquitin or ubiquitin-like modifier (UBL) and a conserved cysteine in an E2 protein, producing reactive ubiquityl units for subsequent ligation to substrate lysines. Two important E1 reaction intermediates have been identified: a ubiquityl-adenylate phosphoester and a ubiquityl-enzyme thioester. However, the mechanism of thioester bond formation and its subsequent transfer to an E2 enzyme remains poorly understood. We have determined the crystal structure of the human UFM1 (ubiquitin-fold modifier 1) E1-activating enzyme UBA5, bound to ATP, revealing a structure that shares similarities with both large canonical E1 enzymes and smaller ancestral E1-like enzymes. In contrast to other E1 active site cysteines, which are in a variably sized domain that is separate and flexible relative to the adenylation domain, the catalytic cysteine of UBA5 (Cys(250)) is part of the adenylation domain in an alpha-helical motif. The novel position of the UBA5 catalytic cysteine and conformational changes associated with ATP binding provides insight into the possible mechanisms through which the ubiquityl-enzyme thioester is formed. These studies reveal structural features that further our understanding of the UBA5 enzyme reaction mechanism and provide insight into the evolution of ubiquitin activation.
Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme.,Bacik JP, Walker JR, Ali M, Schimmer AD, Dhe-Paganon S J Biol Chem. 2010 Jun 25;285(26):20273-80. Epub 2010 Apr 5. PMID:20368332[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Komatsu M, Chiba T, Tatsumi K, Iemura S, Tanida I, Okazaki N, Ueno T, Kominami E, Natsume T, Tanaka K. A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier. EMBO J. 2004 May 5;23(9):1977-86. Epub 2004 Apr 8. PMID:15071506 doi:http://dx.doi.org/10.1038/sj.emboj.7600205
- ↑ Zheng M, Gu X, Zheng D, Yang Z, Li F, Zhao J, Xie Y, Ji C, Mao Y. UBE1DC1, an ubiquitin-activating enzyme, activates two different ubiquitin-like proteins. J Cell Biochem. 2008 Aug 15;104(6):2324-34. doi: 10.1002/jcb.21791. PMID:18442052 doi:http://dx.doi.org/10.1002/jcb.21791
- ↑ Bacik JP, Walker JR, Ali M, Schimmer AD, Dhe-Paganon S. Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme. J Biol Chem. 2010 Jun 25;285(26):20273-80. Epub 2010 Apr 5. PMID:20368332 doi:10.1074/jbc.M110.102921
- ↑ Bacik JP, Walker JR, Ali M, Schimmer AD, Dhe-Paganon S. Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme. J Biol Chem. 2010 Jun 25;285(26):20273-80. Epub 2010 Apr 5. PMID:20368332 doi:10.1074/jbc.M110.102921
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