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| | ==Crystal structure of diaminopimelate epimerase Mycobacterium tuberculosis DapF== | | ==Crystal structure of diaminopimelate epimerase Mycobacterium tuberculosis DapF== |
| - | <StructureSection load='3fve' size='340' side='right' caption='[[3fve]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='3fve' size='340' side='right'caption='[[3fve]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3fve]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FVE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3fve]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FVE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapF, MT2798, MTCY154.06c, Rv2726c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapF, MT2798, MTCY154.06c, Rv2726c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fve OCA], [http://pdbe.org/3fve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fve RCSB], [http://www.ebi.ac.uk/pdbsum/3fve PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fve 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=3fve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fve OCA], [https://pdbe.org/3fve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fve RCSB], [https://www.ebi.ac.uk/pdbsum/3fve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fve ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DAPF_MYCTU DAPF_MYCTU]] 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.<ref>PMID:16907737</ref> <ref>PMID:18269631</ref> | + | [[https://www.uniprot.org/uniprot/DAPF_MYCTU DAPF_MYCTU]] 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.<ref>PMID:16907737</ref> <ref>PMID:18269631</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Diaminopimelate epimerase]] | | [[Category: Diaminopimelate epimerase]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Besra, G S]] | | [[Category: Besra, G S]] |
| | [[Category: Dover, L G]] | | [[Category: Dover, L G]] |
| Structural highlights
3fve is a 1 chain structure with sequence from "bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , |
| Gene: | dapF, MT2798, MTCY154.06c, Rv2726c ("Bacillus tuberculosis" (Zopf 1883) Klein 1884) |
| Activity: | Diaminopimelate epimerase, with EC number 5.1.1.7 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[DAPF_MYCTU] 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.[1] [2]
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
The meso (or D,L) isomer of diaminopimelic acid (DAP), a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan. While the peptidoglycan incorporated in the highly complex cell wall of the pathogen Mycobacterium tuberculosis structurally resembles that of Escherichia coli, it is unique in that it can contain penicillin-resistant meso-DAP-->meso-DAP linkages. The interconversion of L,L-DAP and meso-DAP is catalysed by the DAP epimerase DapF, a gene product that is essential in M. tuberculosis. Here, the crystal structure of the ligand-free form of M. tuberculosis DapF (MtDapF) refined to a resolution of 2.6 A is reported. MtDapF shows small if distinct deviations in secondary structure from the two-domain alpha/beta-fold of the known structures of Haemophilus influenzae DapF and Bacillus anthracis DapF, which are in line with its low sequence identity (<or=27%) to the former. Modelling the present structure onto that of L,L-aziridino-DAP-bound H. influenzae DapF illustrates that a rigid-body movement of domain II and a rearrangement of the B4-A2 loop (residues 80-90) of domain I are likely to accompany the transition from the present inactive form to a catalytically competent enzyme. Despite a highly conserved active-site architecture, the model indicates that stabilization of the DAP backbone occurs in MtDapF through a tyrosine residue that is specific to mycobacterial DAP epimerases.
Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis.,Usha V, Dover LG, Roper DI, Futterer K, Besra GS Acta Crystallogr D Biol Crystallogr. 2009 Apr;65(Pt 4):383-7. Epub 2009, Mar 19. PMID:19307721[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Usha V, Dover LG, Roper DL, Lloyd AJ, Besra GS. Use of a codon alteration strategy in a novel approach to cloning the Mycobacterium tuberculosis diaminopimelic acid epimerase. FEMS Microbiol Lett. 2006 Sep;262(1):39-47. PMID:16907737 doi:http://dx.doi.org/10.1111/j.1574-6968.2006.00356.x
- ↑ Usha V, Dover LG, Roper DL, Besra GS. Characterization of Mycobacterium tuberculosis diaminopimelic acid epimerase: paired cysteine residues are crucial for racemization. FEMS Microbiol Lett. 2008 Mar;280(1):57-63. doi:, 10.1111/j.1574-6968.2007.01049.x. PMID:18269631 doi:http://dx.doi.org/10.1111/j.1574-6968.2007.01049.x
- ↑ Usha V, Dover LG, Roper DI, Futterer K, Besra GS. Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis. Acta Crystallogr D Biol Crystallogr. 2009 Apr;65(Pt 4):383-7. Epub 2009, Mar 19. PMID:19307721 doi:http://dx.doi.org/S0907444909002522
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