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| | <StructureSection load='3zi4' size='340' side='right'caption='[[3zi4]], [[Resolution|resolution]] 1.33Å' scene=''> | | <StructureSection load='3zi4' size='340' side='right'caption='[[3zi4]], [[Resolution|resolution]] 1.33Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3zi4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_lactis"_lister_1873 "bacterium lactis" lister 1873]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZI4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZI4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3zi4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZI4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BG6:BETA-D-GLUCOSE-6-PHOSPHATE'>BG6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SFL:SCANDIUM+TETRAFLOURIDE'>SFL</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]] 1.33Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-phosphoglucomutase Beta-phosphoglucomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.6 5.4.2.6] </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=3zi4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zi4 OCA], [https://pdbe.org/3zi4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zi4 RCSB], [https://www.ebi.ac.uk/pdbsum/3zi4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zi4 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=3zi4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zi4 OCA], [http://pdbe.org/3zi4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zi4 RCSB], [http://www.ebi.ac.uk/pdbsum/3zi4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zi4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PGMB_LACLA PGMB_LACLA]] Catalyzes the interconversion of D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), forming beta-D-glucose 1,6-(bis)phosphate (beta-G16P) as an intermediate. The beta-phosphoglucomutase (Beta-PGM) acts on the beta-C(1) anomer of G1P. Glucose or lactose are used in preference to maltose, which is only utilized after glucose or lactose has been exhausted. It plays a key role in the regulation of the flow of carbohydrate intermediates in glycolysis and the formation of the sugar nucleotide UDP-glucose.<ref>PMID:9084169</ref> <ref>PMID:15005616</ref> | + | [https://www.uniprot.org/uniprot/PGMB_LACLA PGMB_LACLA] Catalyzes the interconversion of D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), forming beta-D-glucose 1,6-(bis)phosphate (beta-G16P) as an intermediate. The beta-phosphoglucomutase (Beta-PGM) acts on the beta-C(1) anomer of G1P. Glucose or lactose are used in preference to maltose, which is only utilized after glucose or lactose has been exhausted. It plays a key role in the regulation of the flow of carbohydrate intermediates in glycolysis and the formation of the sugar nucleotide UDP-glucose.<ref>PMID:9084169</ref> <ref>PMID:15005616</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Enzymes facilitating the transfer of phosphate groups constitute the most extensive protein families across all kingdoms of life. They make up approximately 10% of the proteins found in the human genome. Understanding the mechanisms by which enzymes catalyze these reactions is essential in characterizing the processes they regulate. Metal fluorides can be used as multifunctional tools to study these enzymes. These ionic species bear the same charge as phosphate and the transferring phosphoryl group and, in addition, allow the enzyme to be trapped in catalytically important states with spectroscopically sensitive atoms interacting directly with active site residues. The ionic nature of these phosphate surrogates also allows their removal and replacement with other analogs. Here, we describe the best practices to obtain these complexes, their use in NMR, X-ray crystallography, cryo-EM, and SAXS and describe a new metal fluoride, scandium tetrafluoride, which has significant anomalous signal using soft X-rays. |
| | + | |
| | + | Metal fluorides-multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide.,Pellegrini E, Juyoux P, von Velsen J, Baxter NJ, Dannatt HRW, Jin Y, Cliff MJ, Waltho JP, Bowler MW Structure. 2024 Jul 22:S0969-2126(24)00270-3. doi: 10.1016/j.str.2024.07.007. PMID:39106858<ref>PMID:39106858</ref> |
| | + | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 3zi4" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacterium lactis lister 1873]] | + | [[Category: Lactococcus lactis]] |
| - | [[Category: Beta-phosphoglucomutase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bowler, M W]] | + | [[Category: Bowler MW]] |
| - | [[Category: Pellegrini, E]] | + | [[Category: Pellegrini E]] |
| - | [[Category: Experimental phasing]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Phosphoryl transfer]]
| + | |
| - | [[Category: Scandium tetrafluoride]]
| + | |
| Structural highlights
Function
PGMB_LACLA Catalyzes the interconversion of D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), forming beta-D-glucose 1,6-(bis)phosphate (beta-G16P) as an intermediate. The beta-phosphoglucomutase (Beta-PGM) acts on the beta-C(1) anomer of G1P. Glucose or lactose are used in preference to maltose, which is only utilized after glucose or lactose has been exhausted. It plays a key role in the regulation of the flow of carbohydrate intermediates in glycolysis and the formation of the sugar nucleotide UDP-glucose.[1] [2]
Publication Abstract from PubMed
Enzymes facilitating the transfer of phosphate groups constitute the most extensive protein families across all kingdoms of life. They make up approximately 10% of the proteins found in the human genome. Understanding the mechanisms by which enzymes catalyze these reactions is essential in characterizing the processes they regulate. Metal fluorides can be used as multifunctional tools to study these enzymes. These ionic species bear the same charge as phosphate and the transferring phosphoryl group and, in addition, allow the enzyme to be trapped in catalytically important states with spectroscopically sensitive atoms interacting directly with active site residues. The ionic nature of these phosphate surrogates also allows their removal and replacement with other analogs. Here, we describe the best practices to obtain these complexes, their use in NMR, X-ray crystallography, cryo-EM, and SAXS and describe a new metal fluoride, scandium tetrafluoride, which has significant anomalous signal using soft X-rays.
Metal fluorides-multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide.,Pellegrini E, Juyoux P, von Velsen J, Baxter NJ, Dannatt HRW, Jin Y, Cliff MJ, Waltho JP, Bowler MW Structure. 2024 Jul 22:S0969-2126(24)00270-3. doi: 10.1016/j.str.2024.07.007. PMID:39106858[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Qian N, Stanley GA, Bunte A, Radstrom P. Product formation and phosphoglucomutase activities in Lactococcus lactis: cloning and characterization of a novel phosphoglucomutase gene. Microbiology. 1997 Mar;143 ( Pt 3):855-65. PMID:9084169
- ↑ Lahiri SD, Zhang G, Dai J, Dunaway-Mariano D, Allen KN. Analysis of the substrate specificity loop of the HAD superfamily cap domain. Biochemistry. 2004 Mar 16;43(10):2812-20. PMID:15005616 doi:10.1021/bi0356810
- ↑ Pellegrini E, Juyoux P, von Velsen J, Baxter NJ, Dannatt HRW, Jin Y, Cliff MJ, Waltho JP, Bowler MW. Metal fluorides-multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide. Structure. 2024 Jul 22:S0969-2126(24)00270-3. PMID:39106858 doi:10.1016/j.str.2024.07.007
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