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| | ==Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis== | | ==Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis== |
| - | <StructureSection load='4del' size='340' side='right' caption='[[4del]], [[Resolution|resolution]] 1.58Å' scene=''> | + | <StructureSection load='4del' size='340' side='right'caption='[[4del]], [[Resolution|resolution]] 1.58Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4del]] 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=4DEL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DEL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4del]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DEL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PGH:PHOSPHOGLYCOLOHYDROXAMIC+ACID'>PGH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PGH:PHOSPHOGLYCOLOHYDROXAMIC+ACID'>PGH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ekl|3ekl]], [[3ekz|3ekz]], [[3elf|3elf]], [[4def|4def]]</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=4del FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4del OCA], [https://pdbe.org/4del PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4del RCSB], [https://www.ebi.ac.uk/pdbsum/4del PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4del ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fba, MT0379, MTCY13E10.25c, Rv0363c ([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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphate_aldolase Fructose-bisphosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.13 4.1.2.13] </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=4del FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4del OCA], [http://pdbe.org/4del PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4del RCSB], [http://www.ebi.ac.uk/pdbsum/4del PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4del ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ALF_MYCTU ALF_MYCTU]] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity). | + | [[https://www.uniprot.org/uniprot/ALF_MYCTU ALF_MYCTU]] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Aldolase|Aldolase]] | + | *[[Aldolase 3D structures|Aldolase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Fructose-bisphosphate aldolase]] | + | [[Category: Large Structures]] |
| - | [[Category: Mesecar, A D]] | + | [[Category: Mycobacterium tuberculosis]] |
| - | [[Category: Pegan, S D]] | + | [[Category: Mesecar AD]] |
| - | [[Category: 6-bisphosphate aldolase]] | + | [[Category: Pegan SD]] |
| - | [[Category: Aldol condensation]]
| + | |
| - | [[Category: Class ii fructose-1]]
| + | |
| - | [[Category: Dihydroxyacetone]]
| + | |
| - | [[Category: Glyceraldehyde-3-phosphate]]
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| - | [[Category: Glycolysis]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Phosphoglycolohydroxamate]]
| + | |
| - | [[Category: Zinc enzyme]]
| + | |
| Structural highlights
Function
[ALF_MYCTU] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity).
Publication Abstract from PubMed
Class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff base intermediate using an epsilon-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation-deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA-PGH complex to 1.58 A. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation-protonation step of the MtFBA reaction mechanism. Also, secondary isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.
Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis.,Pegan SD, Rukseree K, Capodagli GC, Baker EA, Krasnykh O, Franzblau SG, Mesecar AD Biochemistry. 2013 Jan 18. PMID:23298222[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Pegan SD, Rukseree K, Capodagli GC, Baker EA, Krasnykh O, Franzblau SG, Mesecar AD. Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis. Biochemistry. 2013 Jan 18. PMID:23298222 doi:10.1021/bi300928u
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