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| | ==Crystal structure of H136A mutant of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate== | | ==Crystal structure of H136A mutant of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate== |
| - | <StructureSection load='1so3' size='340' side='right' caption='[[1so3]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='1so3' size='340' side='right'caption='[[1so3]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1so3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SO3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SO3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1so3]] is a 2 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=1SO3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SO3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TX4:L-THREONOHYDROXAMATE+4-PHOSPHATE'>TX4</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1q6l|1q6l]], [[1q6o|1q6o]], [[1q6q|1q6q]], [[1q6r|1q6r]], [[1so4|1so4]], [[1so5|1so5]], [[1so6|1so6]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TX4:L-THREONOHYDROXAMATE+4-PHOSPHATE'>TX4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UlaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1so3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1so3 OCA], [https://pdbe.org/1so3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1so3 RCSB], [https://www.ebi.ac.uk/pdbsum/1so3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1so3 ProSAT]</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=1so3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1so3 OCA], [http://pdbe.org/1so3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1so3 RCSB], [http://www.ebi.ac.uk/pdbsum/1so3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1so3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ULAD_ECOLI ULAD_ECOLI]] Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.<ref>PMID:11741871</ref> | + | [https://www.uniprot.org/uniprot/ULAD_ECOLI ULAD_ECOLI] Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.<ref>PMID:11741871</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/so/1so3_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/so/1so3_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Gerlt, J A]] | + | [[Category: Large Structures]] |
| - | [[Category: Rayment, I]] | + | [[Category: Gerlt JA]] |
| - | [[Category: Wise, E L]] | + | [[Category: Rayment I]] |
| - | [[Category: Yew, W S]] | + | [[Category: Wise EL]] |
| - | [[Category: Beta barrel]] | + | [[Category: Yew WS]] |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
ULAD_ECOLI Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.[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
3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC), a member of the orotidine monophosphate decarboxylase (OMPDC) suprafamily, catalyzes the Mg(2+)-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to L-xylulose 5-phosphate. Structural and biochemical evidence suggests that the KGPDC reaction proceeds via a Mg(2+)-stabilized 1,2-cis-enediolate intermediate. Protonation of the enediolate intermediate occurs in a nonstereospecific manner to form L-xylulose 5-phosphate. Although the exact mechanism of proton delivery is not known, Glu112, His136, and Arg139 have been implicated in this process [Yew, W. S., Wise, E., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 43, 6427-6437]. Surprisingly, single amino acid substitutions of these positions do not substantially reduce catalytic activity but rather alter the stereochemical course of the reaction. Here, we report the X-ray crystal structures of four mutants, K64A, H136A, E112Q, and E112Q/H136A, each determined in the presence of L-threonohydroxamate 4-phosphate, an analogue of the enediolate intermediate, to 1.7, 1.9, 1.8, and 1.9 A resolution, respectively. These structures reveal that substitutions of Lys64, Glu112, and His136 cause changes in the positions of the intermediate analogue and two active site water molecules that were previously identified as possible proton donors. These changes correlate with the observed alterations in the reaction stereochemistry for these mutants, thereby supporting a reaction mechanism in which water molecules competitively shuttle protons from the side chains of His136 and Arg139 to alternate faces of the cis-enediolate intermediate. These studies further underscore the wide variation in the reaction mechanisms in the OMPDC suprafamily.
Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase.,Wise EL, Yew WS, Gerlt JA, Rayment I Biochemistry. 2004 Jun 1;43(21):6438-46. PMID:15157078[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yew WS, Gerlt JA. Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons. J Bacteriol. 2002 Jan;184(1):302-6. PMID:11741871
- ↑ Wise EL, Yew WS, Gerlt JA, Rayment I. Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry. 2004 Jun 1;43(21):6438-46. PMID:15157078 doi:10.1021/bi0497392
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