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| | ==x-ray crystal structure of Staphylococcus aureus MurE with UDP-MurNAc- Ala-Glu-Lys== | | ==x-ray crystal structure of Staphylococcus aureus MurE with UDP-MurNAc- Ala-Glu-Lys== |
| - | <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/Staphylococcus_aureus Staphylococcus aureus]. 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</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='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=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4c12|4c12]]</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> |
| - | <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='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> | + | |
| | </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/MURE_STAA8 MURE_STAA8] 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. Can not use diaminopimelate as substrate. Seems to have a role in beta-lactam antibiotic resistance.<ref>PMID:14114846</ref> <ref>PMID:10498701</ref> <ref>PMID:14996801</ref> |
| | <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> |
| | </div> | | </div> |
| | <div class="pdbe-citations 4c13" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4c13" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Mur ligase|Mur ligase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase]] | + | [[Category: Large Structures]] |
| - | [[Category: Barreteau, H]] | + | [[Category: Staphylococcus aureus]] |
| - | [[Category: Blanot, D]] | + | [[Category: Barreteau H]] |
| - | [[Category: Boniface, A]] | + | [[Category: Blanot D]] |
| - | [[Category: Dementin, S]] | + | [[Category: Boniface A]] |
| - | [[Category: Dessen, A]] | + | [[Category: Dementin S]] |
| - | [[Category: Dowson, C G]] | + | [[Category: Dessen A]] |
| - | [[Category: Fulop, V]] | + | [[Category: Dowson CG]] |
| - | [[Category: Gobec, S]] | + | [[Category: Fulop V]] |
| - | [[Category: Lloyd, A J]] | + | [[Category: Gobec S]] |
| - | [[Category: Mengin-Lecreulx, D]] | + | [[Category: Lloyd AJ]] |
| - | [[Category: Roper, D I]] | + | [[Category: Mengin-Lecreulx D]] |
| - | [[Category: Ruane, K M]] | + | [[Category: Roper DI]] |
| - | [[Category: Ligase]]
| + | [[Category: Ruane KM]] |
| - | [[Category: Mure]]
| + | |
| Structural highlights
4c13 is a 1 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.9Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
MURE_STAA8 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. Can not use diaminopimelate as substrate. Seems to have a role in beta-lactam antibiotic resistance.[1] [2] [3]
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[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ ITO E, STROMINGER JL. ENZYMATIC SYNTHESIS OF THE PEPTIDE IN BACTERIAL URIDINE NUCLEOTIDES. III. PURIFICATION AND PROPERTIES OF L-LYSIN-ADDING ENZYME. J Biol Chem. 1964 Jan;239:210-4. PMID:14114846
- ↑ Mengin-Lecreulx D, Falla T, Blanot D, van Heijenoort J, Adams DJ, Chopra I. Expression of the Staphylococcus aureus UDP-N-acetylmuramoyl- L-alanyl-D-glutamate:L-lysine ligase in Escherichia coli and effects on peptidoglycan biosynthesis and cell growth. J Bacteriol. 1999 Oct;181(19):5909-14. PMID:10498701
- ↑ Gardete S, Ludovice AM, Sobral RG, Filipe SR, de Lencastre H, Tomasz A. Role of murE in the Expression of beta-lactam antibiotic resistance in Staphylococcus aureus. J Bacteriol. 2004 Mar;186(6):1705-13. PMID:14996801
- ↑ 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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