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| | ==Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin== | | ==Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin== |
| - | <StructureSection load='6dc6' size='340' side='right' caption='[[6dc6]], [[Resolution|resolution]] 3.14Å' scene=''> | + | <StructureSection load='6dc6' size='340' side='right'caption='[[6dc6]], [[Resolution|resolution]] 3.14Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6dc6]] is a 4 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=6DC6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DC6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6dc6]] is a 4 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=6DC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DC6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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]] 3.14Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBA1, A1S9T, UBE1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E1_ubiquitin-activating_enzyme E1 ubiquitin-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.45 6.2.1.45] </span></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=6dc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dc6 OCA], [https://pdbe.org/6dc6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dc6 RCSB], [https://www.ebi.ac.uk/pdbsum/6dc6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dc6 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=6dc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dc6 OCA], [http://pdbe.org/6dc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dc6 RCSB], [http://www.ebi.ac.uk/pdbsum/6dc6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dc6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Disease == | | == Disease == |
| - | [[http://www.uniprot.org/uniprot/UBA1_HUMAN UBA1_HUMAN]] X-linked distal arthrogryposis multiplex congenita. The disease is caused by mutations affecting the gene represented in this entry. | + | [https://www.uniprot.org/uniprot/UBA1_HUMAN UBA1_HUMAN] X-linked distal arthrogryposis multiplex congenita. The disease is caused by mutations affecting the gene represented in this entry. |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/UBA1_HUMAN UBA1_HUMAN]] Catalyzes the first step in ubiquitin conjugation to mark cellular proteins for degradation through the ubiquitin-proteasome system. Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding a ubiquitin-E1 thioester and free AMP. Essential for the formation of radiation-induced foci, timely DNA repair and for response to replication stress. Promotes the recruitment of TP53BP1 and BRCA1 at DNA damage sites.<ref>PMID:22456334</ref> [[http://www.uniprot.org/uniprot/RS27A_HUMAN RS27A_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref> Ribosomal protein S27a is a component of the 40S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref> | + | [https://www.uniprot.org/uniprot/UBA1_HUMAN UBA1_HUMAN] Catalyzes the first step in ubiquitin conjugation to mark cellular proteins for degradation through the ubiquitin-proteasome system. Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding a ubiquitin-E1 thioester and free AMP. Essential for the formation of radiation-induced foci, timely DNA repair and for response to replication stress. Promotes the recruitment of TP53BP1 and BRCA1 at DNA damage sites.<ref>PMID:22456334</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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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]] |
| | + | *[[3D structures of ubiquitin|3D structures of ubiquitin]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: E1 ubiquitin-activating enzyme]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Human]] | + | [[Category: Large Structures]] |
| - | [[Category: Atkison, J H]] | + | [[Category: Atkison JH]] |
| - | [[Category: Lv, Z]] | + | [[Category: Lv Z]] |
| - | [[Category: Olsen, S K]] | + | [[Category: Olsen SK]] |
| - | [[Category: Williams, K M]] | + | [[Category: Williams KM]] |
| - | [[Category: Yuan, L]] | + | [[Category: Yuan L]] |
| - | [[Category: Adenylation]]
| + | |
| - | [[Category: E1]]
| + | |
| - | [[Category: E2]]
| + | |
| - | [[Category: Signaling protein]]
| + | |
| - | [[Category: Signaling protein-ligase complex]]
| + | |
| - | [[Category: Thioester bond]]
| + | |
| - | [[Category: Transthiolation]]
| + | |
| - | [[Category: Ubiquitin]]
| + | |
| Structural highlights
Disease
UBA1_HUMAN X-linked distal arthrogryposis multiplex congenita. The disease is caused by mutations affecting the gene represented in this entry.
Function
UBA1_HUMAN Catalyzes the first step in ubiquitin conjugation to mark cellular proteins for degradation through the ubiquitin-proteasome system. Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding a ubiquitin-E1 thioester and free AMP. Essential for the formation of radiation-induced foci, timely DNA repair and for response to replication stress. Promotes the recruitment of TP53BP1 and BRCA1 at DNA damage sites.[1]
Publication Abstract from PubMed
Ubiquitin (Ub) signaling plays a key regulatory role in nearly every aspect of eukaryotic biology and is initiated by E1 enzymes that activate and transfer Ub to E2 Ub-conjugating enzymes. Despite Ub E1's fundamental importance to the cell and its attractiveness as a target for therapeutic intervention in cancer and other diseases, its only available structural information is derived from yeast orthologs of human ubiquitin-like modifier-activating enzyme 1 (hUBA1). To illuminate structural differences between yeast and hUBA1 structures that might be exploited for the development of small-molecule therapeutics, we determined the first crystal structure of a hUBA1/Ub complex. Using structural analysis, molecular modeling, and biochemical analysis, we demonstrate that hUBA1 shares a conserved overall structure and mechanism with previously characterized yeast orthologs, but displays subtle structural differences, particularly within the active site. Computational analysis revealed four potential ligand-binding hotspots on the surface of hUBA1 that might serve as targets to inhibit hUBA1 at the level of Ub activation or E2 recruitment or that might potentially be used in approaches such as protein-targeting chimeric molecules (PROTACs). Taken together, our work enhances our understanding of the hUBA1 mechanism, provides an improved framework for the development of small-molecule inhibitors of UBA1, and serves as a stepping stone for structural studies that involve the enzymes of the human Ub system at the level of both E1 and E2.
Crystal structure of a human ubiquitin E1-ubiquitin complex reveals conserved functional elements essential for activity.,Lv Z, Williams KM, Yuan L, Atkison JH, Olsen SK J Biol Chem. 2018 Oct 2. pii: RA118.003975. doi: 10.1074/jbc.RA118.003975. PMID:30279270[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Moudry P, Lukas C, Macurek L, Hanzlikova H, Hodny Z, Lukas J, Bartek J. Ubiquitin-activating enzyme UBA1 is required for cellular response to DNA damage. Cell Cycle. 2012 Apr 15;11(8):1573-82. doi: 10.4161/cc.19978. Epub 2012 Apr 15. PMID:22456334 doi:http://dx.doi.org/10.4161/cc.19978
- ↑ Lv Z, Williams KM, Yuan L, Atkison JH, Olsen SK. Crystal structure of a human ubiquitin E1-ubiquitin complex reveals conserved functional elements essential for activity. J Biol Chem. 2018 Oct 2. pii: RA118.003975. doi: 10.1074/jbc.RA118.003975. PMID:30279270 doi:http://dx.doi.org/10.1074/jbc.RA118.003975
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