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| - | ==Crystal strcuture of reduced DapF from Corynebacterium glutamicum== | + | ==Crystal structure of reduced DapF from Corynebacterium glutamicum== |
| | <StructureSection load='5h2y' size='340' side='right'caption='[[5h2y]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='5h2y' size='340' side='right'caption='[[5h2y]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5h2y]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H2Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5H2Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5h2y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H2Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H2Y FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5h2g|5h2g]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </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=5h2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h2y OCA], [https://pdbe.org/5h2y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h2y RCSB], [https://www.ebi.ac.uk/pdbsum/5h2y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h2y ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5h2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h2y OCA], [http://pdbe.org/5h2y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h2y RCSB], [http://www.ebi.ac.uk/pdbsum/5h2y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h2y ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DAPF_CORGL DAPF_CORGL]] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Involved in the succinylase branch of the diaminopimelate biosynthesis.<ref>PMID:12948639</ref> | + | [https://www.uniprot.org/uniprot/DAPF_CORGL DAPF_CORGL] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Involved in the succinylase branch of the diaminopimelate biosynthesis.<ref>PMID:12948639</ref> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Diaminopimelate epimerase (DapF) is one of the crucial enzymes involved in l-lysine biosynthesis, where it converts l,l-diaminopimelate (l,l-DAP) into d,l-DAP. DapF is also considered as an attractive target for the development of antibacterial drugs. Here, we report the crystal structure of DapF from Corynebacterium glutamicum (CgDapF). Structures of CgDapF obtained under both oxidized and reduced conditions reveal that the function of CgDapF is regulated by redox-switch modulation via reversible disulfide bond formation between two catalytic cysteine residues. Under oxidized condition, two catalytic cysteine residues form a disulfide bond; these same cysteine residues exist in reduced form under reduced condition. Disulfide bond formation also induces a subsequent structural change in the dynamic catalytic loop at the active site, which results in open/closed conformational change at the active site. We also determined the crystal structure of CgDapF in complex with its product d,l-DAP, and elucidated how the enzyme recognizes its substrate l,l-DAP as a substrate. Moreover, the structure in complex with the d,l-DAP product reveals that CgDapF undergoes a large open/closed domain movement upon substrate binding, resulting in a completely buried active site with the substrate bound.
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| - | Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.,Sagong HY, Kim KJ Sci Rep. 2017 Feb 8;7:42318. doi: 10.1038/srep42318. PMID:28176858<ref>PMID:28176858</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 5h2y" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Diaminopimelate epimerase]] | + | [[Category: Corynebacterium glutamicum ATCC 13032]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kim, K J]] | + | [[Category: Kim K-J]] |
| - | [[Category: Sagong, H Y]] | + | [[Category: Sagong H-Y]] |
| - | [[Category: Isomerase]]
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