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| | <StructureSection load='4c13' size='340' side='right'caption='[[4c13]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='4c13' size='340' side='right'caption='[[4c13]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4c13]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4C13 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4c13]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C13 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UML:URIDINE+5DIPHOSPHO+N-ACETYL+MURAMOYL-L-ALANYL-D-GLUTAMYL-L-LYSINE'>UML</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UML:URIDINE+5DIPHOSPHO+N-ACETYL+MURAMOYL-L-ALANYL-D-GLUTAMYL-L-LYSINE'>UML</scene></td></tr> |
| | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4c12|4c12]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4c12|4c12]]</div></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine_ligase UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.7 6.3.2.7] </span></td></tr> | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine_ligase UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.7 6.3.2.7] </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=4c13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c13 OCA], [http://pdbe.org/4c13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4c13 RCSB], [http://www.ebi.ac.uk/pdbsum/4c13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4c13 ProSAT]</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=4c13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c13 OCA], [https://pdbe.org/4c13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c13 RCSB], [https://www.ebi.ac.uk/pdbsum/4c13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c13 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/D4U2M7_STAAU D4U2M7_STAAU]] Catalyzes the addition of L-lysine to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan (By similarity).[HAMAP-Rule:MF_00208] | + | [[https://www.uniprot.org/uniprot/D4U2M7_STAAU D4U2M7_STAAU]] Catalyzes the addition of L-lysine to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan (By similarity).[HAMAP-Rule:MF_00208] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| - | Formation of the peptidoglycan stem pentapeptide requires the insertion of both L or D amino acids by the ATP dependent ligase enzymes MurC, D, E and F. The stereo chemical control of the third position amino acid in the pentapeptide, is crucial to maintain the fidelity of later biosynthetic steps contributing to cell morphology, antibiotic resistance and pathogenesis. Here we determine the X-ray crystal structure of Staphylococcus aureus MurE UDP-N-acetylmuramoyl-l-alanyl-d-glutamate: meso-2,6-diaminopimelate ligase (MurE) (E.C. 6.3.2.15) at 1.8 angstrom resolution in the presence of ADP and the reaction product, UDP-MurNAc-L-Ala-gamma-D-Glu-L-Lys. This structure provides for the first time a molecular understanding of how this Gram-positive enzyme discriminates between L-lysine and D,L-diaminopimelic acid, the predominant amino acid that replaces L-lysine in Gram-negative peptidoglycan. Despite the presence of a consensus sequence previously implicated in the selection of the third position residue in the stem pentapeptide in S. aureus MurE, the structure shows that only part of this sequence is involved in the selection of L-lysine. Instead, other parts of the protein contribute substrate-selecting residues resulting in a lysine-binding pocket based on charge characteristics. Despite the absolute specificity for L-lysine, S. aureus MurE binds this substrate relatively poorly. In-vivo analysis and metabolomic data reveals that this is compensated for by high cytoplasmic L-lysine concentrations. Therefore both metabolic and structural constraints maintain the structural integrity of the staphylococcal peptidoglycan. This study provides a novel focus for S. aureus directed antimicrobials based, on dual targeting of essential amino acid biogenesis and its linkage to cell wall assembly.
| + | The discovery of effective therapeutic treatments for cancer via cell differentiation instead of antiproliferation remains a great challenge. Cyclin-dependent kinase 2 (CDK2) inactivation, which overcomes the differentiation arrest of acute myeloid leukemia (AML) cells, may be a promising method for AML treatment. However, there is no available selective CDK2 inhibitor. More importantly, the inhibition of only the enzymatic function of CDK2 would be insufficient to promote notable AML differentiation. To further validate the role and druggability of CDK2 involved in AML differentiation, a suitable chemical tool is needed. Therefore, we developed first-in-class CDK2-targeted proteolysis-targeting chimeras (PROTACs), which promoted rapid and potent CDK2 degradation in different cell lines without comparable degradation of other targets, and induced remarkable differentiation of AML cell lines and primary patient cells. These data clearly demonstrated the practicality and importance of PROTACs as alternative tools for verifying CDK2 protein functions. |
| | | | |
| - | Specificity Determinants for Lysine Incorporation in Staphylococcus aureus Peptidoglycan as Revealed by the Structure of a MurE Ternary Complex.,Ruane KM, Lloyd AJ, Fulop V, Dowson CG, Barreteau H, Boniface A, Dementin S, Blanot D, Mengin-Lecreulx D, Gobec S, Dessen A, Roper DI J Biol Chem. 2013 Sep 24. PMID:24064214<ref>PMID:24064214</ref>
| + | Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy.,Wang L, Shao X, Zhong T, Wu Y, Xu A, Sun X, Gao H, Liu Y, Lan T, Tong Y, Tao X, Du W, Wang W, Chen Y, Li T, Meng X, Deng H, Yang B, He Q, Ying M, Rao Y Nat Chem Biol. 2021 Mar 4. pii: 10.1038/s41589-021-00742-5. doi:, 10.1038/s41589-021-00742-5. PMID:33664520<ref>PMID:33664520</ref> |
| | | | |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| Structural highlights
4c13 is a 1 chain structure with sequence from "micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , |
| NonStd Res: | |
| Related: | |
| Activity: | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase, with EC number 6.3.2.7 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[D4U2M7_STAAU] Catalyzes the addition of L-lysine to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan (By similarity).[HAMAP-Rule:MF_00208]
Publication Abstract from PubMed
The discovery of effective therapeutic treatments for cancer via cell differentiation instead of antiproliferation remains a great challenge. Cyclin-dependent kinase 2 (CDK2) inactivation, which overcomes the differentiation arrest of acute myeloid leukemia (AML) cells, may be a promising method for AML treatment. However, there is no available selective CDK2 inhibitor. More importantly, the inhibition of only the enzymatic function of CDK2 would be insufficient to promote notable AML differentiation. To further validate the role and druggability of CDK2 involved in AML differentiation, a suitable chemical tool is needed. Therefore, we developed first-in-class CDK2-targeted proteolysis-targeting chimeras (PROTACs), which promoted rapid and potent CDK2 degradation in different cell lines without comparable degradation of other targets, and induced remarkable differentiation of AML cell lines and primary patient cells. These data clearly demonstrated the practicality and importance of PROTACs as alternative tools for verifying CDK2 protein functions.
Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy.,Wang L, Shao X, Zhong T, Wu Y, Xu A, Sun X, Gao H, Liu Y, Lan T, Tong Y, Tao X, Du W, Wang W, Chen Y, Li T, Meng X, Deng H, Yang B, He Q, Ying M, Rao Y Nat Chem Biol. 2021 Mar 4. pii: 10.1038/s41589-021-00742-5. doi:, 10.1038/s41589-021-00742-5. PMID:33664520[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wang L, Shao X, Zhong T, Wu Y, Xu A, Sun X, Gao H, Liu Y, Lan T, Tong Y, Tao X, Du W, Wang W, Chen Y, Li T, Meng X, Deng H, Yang B, He Q, Ying M, Rao Y. Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy. Nat Chem Biol. 2021 Mar 4. pii: 10.1038/s41589-021-00742-5. doi:, 10.1038/s41589-021-00742-5. PMID:33664520 doi:http://dx.doi.org/10.1038/s41589-021-00742-5
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