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| - | [[Image:1ik4.gif|left|200px]] | |
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| - | <!--
| + | ==X-ray Structure of Methylglyoxal Synthase from E. coli Complexed with Phosphoglycolohydroxamic Acid== |
| - | The line below this paragraph, containing "STRUCTURE_1ik4", creates the "Structure Box" on the page.
| + | <StructureSection load='1ik4' size='340' side='right'caption='[[1ik4]], [[Resolution|resolution]] 2.00Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1ik4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IK4 FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGH:PHOSPHOGLYCOLOHYDROXAMIC+ACID'>PGH</scene></td></tr> |
| - | {{STRUCTURE_1ik4| PDB=1ik4 | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ik4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ik4 OCA], [https://pdbe.org/1ik4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ik4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ik4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ik4 ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''X-ray Structure of Methylglyoxal Synthase from E. coli Complexed with Phosphoglycolohydroxamic Acid'''
| + | == Function == |
| - | | + | [https://www.uniprot.org/uniprot/MGSA_ECOLI MGSA_ECOLI] |
| - | | + | == Evolutionary Conservation == |
| - | ==Overview== | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | Methylglyoxal synthase (MGS) and triosephosphate isomerase (TIM) share neither sequence nor structural similarities, yet the reactions catalyzed by both enzymes are similar, in that both initially convert dihydroxyacetone phosphate to a cis-enediolic intermediate. This enediolic intermediate is formed from the abstraction of the pro-S C3 proton of DHAP by Asp-71 of MGS or the pro-R C3 proton of DHAP by Glu-165 of TIM. MGS then catalyzes the elimination of phosphate from this enediolic intermediate to form the enol of methylglyoxal, while TIM catalyzes proton donation to C2 to form D-glyceraldehyde phosphate. A competitive inhibitor of TIM, phosphoglycolohydroxamic acid (PGH) is found to be a tight binding competitive inhibitor of MGS with a K(i) of 39 nM. PGH's high affinity for MGS may be due in part to a short, strong hydrogen bond (SSHB) from the NOH of PGH to the carboxylate of Asp-71. Evidence for this SSHB is found in X-ray, 1H NMR, and fractionation factor data. The X-ray structure of the MGS homohexamer complexed with PGH at 2.0 A resolution shows this distance to be 2.30-2.37 +/- 0.24 A. 1H NMR shows a PGH-dependent 18.1 ppm signal that is consistent with a hydrogen bond length of 2.49 +/- 0.02 A. The D/H fractionation factor (phi = 0.43 +/- 0.02) is consistent with a hydrogen bond length of 2.53 +/- 0.01 A. Further, 15N NMR suggests a significant partial positive charge on the nitrogen atom of bound PGH, which could strengthen hydrogen bond donation to Asp-71. Both His-98 and His-19 are uncharged in the MGS-PGH complex on the basis of the chemical shifts of their Cdelta and C(epsilon) protons. The crystal structure reveals that Asp-71, on the re face of PGH, and His-19, on the si face of PGH, both approach the NO group of the analogue, while His-98, in the plane of PGH, approaches the carbonyl oxygen of the analogue. The phosphate group of PGH accepts nine hydrogen bonds from seven residues and is tilted out of the imidate plane of PGH toward the re face. Asp-71 and phosphate are thus positioned to function as the base and leaving group, respectively, in a concerted suprafacial 1,4-elimination of phosphate from the enediolic intermediate in the second step of the MGS reaction. Combined, these data suggest that Asp-71 is the one base that initially abstracts the C3 pro-S proton from DHAP and subsequently the 3-OH proton from the enediolic intermediate. This mechanism is compared to an alternative TIM-like mechanism for MGS, and the relative merits of both mechanisms are discussed.
| + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==About this Structure== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/1ik4_consurf.spt"</scriptWhenChecked> |
| - | 1IK4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IK4 OCA].
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==Reference== | + | </jmolCheckbox> |
| - | Mechanistic implications of methylglyoxal synthase complexed with phosphoglycolohydroxamic acid as observed by X-ray crystallography and NMR spectroscopy., Marks GT, Harris TK, Massiah MA, Mildvan AS, Harrison DH, Biochemistry. 2001 Jun 12;40(23):6805-18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11389594 11389594]
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ik4 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Methylglyoxal synthase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Harris TK]] |
| - | [[Category: Harris, T K.]] | + | [[Category: Harrison DHT]] |
| - | [[Category: Harrison, D H.T.]] | + | [[Category: Marks GT]] |
| - | [[Category: Marks, G T.]] | + | [[Category: Massiah MA]] |
| - | [[Category: Massiah, M A.]] | + | [[Category: Mildvan AS]] |
| - | [[Category: Mildvan, A S.]] | + | |
| - | [[Category: Glycolytic bypass]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Methylglyoxal]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:05:22 2008''
| + | |
