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| | <StructureSection load='2q9h' size='340' side='right'caption='[[2q9h]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='2q9h' size='340' side='right'caption='[[2q9h]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2q9h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q9H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2q9h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q9H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2gke|2gke]], [[2gkj|2gkj]], [[1gqz|1gqz]], [[1bwz|1bwz]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [https://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=2q9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9h OCA], [https://pdbe.org/2q9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q9h RCSB], [https://www.ebi.ac.uk/pdbsum/2q9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q9h 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=2q9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9h OCA], [https://pdbe.org/2q9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q9h RCSB], [https://www.ebi.ac.uk/pdbsum/2q9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q9h ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DAPF_HAEIN DAPF_HAEIN]] 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. Only accepts DAP isomers with the L configuration.<ref>PMID:10194362</ref>
| + | [https://www.uniprot.org/uniprot/DAPF_HAEIN DAPF_HAEIN] 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. Only accepts DAP isomers with the L configuration.<ref>PMID:10194362</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacterium influenzae lehmann and neumann 1896]] | + | [[Category: Haemophilus influenzae]] |
| - | [[Category: Diaminopimelate epimerase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Blanchard, J S]] | + | [[Category: Blanchard JS]] |
| - | [[Category: Cherney, M]] | + | [[Category: Cherney M]] |
| - | [[Category: Diaper, C M]] | + | [[Category: Diaper CM]] |
| - | [[Category: James, M N.G]] | + | [[Category: James MNG]] |
| - | [[Category: Pillai, B]] | + | [[Category: Pillai B]] |
| - | [[Category: Sutherland, A]] | + | [[Category: Sutherland A]] |
| - | [[Category: Vederas, J C]] | + | [[Category: Vederas JC]] |
| - | [[Category: Apo form has an open conformation]]
| + | |
| - | [[Category: C73s mutant]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Two structurally equivalent domain]]
| + | |
| Structural highlights
Function
DAPF_HAEIN 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. Only accepts DAP isomers with the L configuration.[1]
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
Diaminopimelate (DAP) epimerase catalyzes the stereoinversion of ll-DAP to meso-DAP, a precursor of l-lysine and an essential component of the bacterial peptidoglycan. This function is vital to bacteria and the enzyme therefore represents an attractive target for the design of novel anti-bacterials. DAP epimerase belongs to the group of PLP-independent amino acid racemases that function through a rather unusual mechanism involving two cysteines acting in concert as a base (thiolate) and an acid (thiol). We have solved the crystal structures of the apo-forms of DAP epimerase mutants (C73S and C217S) from Haemophilus influenzae at 2.3A and 2.2A resolution, respectively. These structures provide a snapshot of the enzyme in the first step of the catalytic cycle. Comparisons with the structures of the inhibitor-bound form reveal that the enzyme adopts an 'open conformation' in the absence of substrates or inhibitors with the two active site cysteines existing as a thiol-thiolate pair. Substrate binding to the C-terminal domain triggers the closure of the N-terminal domain coupled with tight encapsulation of the ligand, stabilization of the conformation of an active site loop containing Cys73 and expulsion of water molecules with concomitant desolvation of the thiolate base. This structural rearrangement is critical for catalysis.
Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase.,Pillai B, Cherney M, Diaper CM, Sutherland A, Blanchard JS, Vederas JC, James MN Biochem Biophys Res Commun. 2007 Nov 23;363(3):547-53. Epub 2007 Sep 17. PMID:17889830[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Koo CW, Blanchard JS. Chemical mechanism of Haemophilus influenzae diaminopimelate epimerase. Biochemistry. 1999 Apr 6;38(14):4416-22. PMID:10194362 doi:http://dx.doi.org/10.1021/bi982911f
- ↑ Pillai B, Cherney M, Diaper CM, Sutherland A, Blanchard JS, Vederas JC, James MN. Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase. Biochem Biophys Res Commun. 2007 Nov 23;363(3):547-53. Epub 2007 Sep 17. PMID:17889830 doi:http://dx.doi.org/10.1016/j.bbrc.2007.09.012
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