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| | ==Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli complexed with magnesium and phosphate== | | ==Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli complexed with magnesium and phosphate== |
| - | <StructureSection load='3l8f' size='340' side='right' caption='[[3l8f]], [[Resolution|resolution]] 1.79Å' scene=''> | + | <StructureSection load='3l8f' size='340' side='right'caption='[[3l8f]], [[Resolution|resolution]] 1.79Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3l8f]] is a 1 chain structure with 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=3L8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L8F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3l8f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L8F 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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.79Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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">[[3l8e|3l8e]], [[3l8g|3l8g]], [[3l8h|3l8h]]</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=3l8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l8f OCA], [https://pdbe.org/3l8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l8f RCSB], [https://www.ebi.ac.uk/pdbsum/3l8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l8f ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0200, gmhB, JW0196, yaeD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
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| - | <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=3l8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l8f RCSB], [http://www.ebi.ac.uk/pdbsum/3l8f PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/GMHBB_ECOLI GMHBB_ECOLI] Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate (beta-HBP) intermediate into D-glycero-beta-D-manno-heptose 1-phosphate by removing the phosphate group at the C-7 position.<ref>PMID:11751812</ref> <ref>PMID:16990279</ref> <ref>PMID:20050615</ref> <ref>PMID:31449400</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l8/3l8f_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l8/3l8f_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> |
| - | </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/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </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=3l8f ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3l8f" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Allen, K N]]
| + | [[Category: Large Structures]] |
| - | [[Category: Nguyen, H]]
| + | [[Category: Allen KN]] |
| - | [[Category: Peisach, E]]
| + | [[Category: Nguyen H]] |
| - | [[Category: 7-bisphosphate phosphatase]]
| + | [[Category: Peisach E]] |
| - | [[Category: Carbohydrate metabolism]] | + | |
| - | [[Category: D-glycero-d-manno-heptose-1]] | + | |
| - | [[Category: Gmhb]] | + | |
| - | [[Category: Had superfamily]] | + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lipopolysaccharide biosynthesis]]
| + | |
| Structural highlights
Function
GMHBB_ECOLI Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate (beta-HBP) intermediate into D-glycero-beta-D-manno-heptose 1-phosphate by removing the phosphate group at the C-7 position.[1] [2] [3] [4]
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 haloalkanoic acid dehalogenase (HAD) enzyme superfamily is the largest family of phosphohydrolases. In HAD members, the structural elements that provide the binding interactions that support substrate specificity are separated from those that orchestrate catalysis. For most HAD phosphatases, a cap domain functions in substrate recognition. However, for the HAD phosphatases that lack a cap domain, an alternate strategy for substrate selection must be operative. One such HAD phosphatase, GmhB of the HisB subfamily, was selected for structure-function analysis. Herein, the X-ray crystallographic structures of Escherichia coli GmhB in the apo form (1.6 A resolution), in a complex with Mg(2+) and orthophosphate (1.8 A resolution), and in a complex with Mg(2+) and d-glycero-d-manno-heptose 1beta,7-bisphosphate (2.2 A resolution) were determined, in addition to the structure of Bordetella bronchiseptica GmhB bound to Mg(2+) and orthophosphate (1.7 A resolution). The structures show that in place of a cap domain, the GmhB catalytic site is elaborated by three peptide inserts or loops that pack to form a concave, semicircular surface around the substrate leaving group. Structure-guided kinetic analysis of site-directed mutants was conducted in parallel with a bioinformatics study of sequence diversification within the HisB subfamily to identify loop residues that serve as substrate recognition elements and that distinguish GmhB from its subfamily counterpart, the histidinol-phosphate phosphatase domain of HisB. We show that GmhB and the histidinol-phosphate phosphatase domain use the same design of three substrate recognition loops inserted into the cap domain yet, through selective residue usage on the loops, have achieved unique substrate specificity and thus novel biochemical function.
Structural Determinants of Substrate Recognition in the HAD Superfamily Member d-glycero-d-manno-Heptose-1,7-bisphosphate Phosphatase (GmhB) .,Nguyen HH, Wang L, Huang H, Peisach E, Dunaway-Mariano D, Allen KN Biochemistry. 2010 Jan 22. PMID:20050614[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kneidinger B, Marolda C, Graninger M, Zamyatina A, McArthur F, Kosma P, Valvano MA, Messner P. Biosynthesis pathway of ADP-L-glycero-beta-D-manno-heptose in Escherichia coli. J Bacteriol. 2002 Jan;184(2):363-9. PMID:11751812
- ↑ Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem. 2006 Nov 24;281(47):36149-61. Epub 2006 Sep 21. PMID:16990279 doi:10.1074/jbc.M605449200
- ↑ Wang L, Huang H, Nguyen HH, Allen KN, Mariano PS, Dunaway-Mariano D. Divergence of biochemical function in the HAD superfamily: D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB). Biochemistry. 2010 Feb 16;49(6):1072-81. doi: 10.1021/bi902018y. PMID:20050615 doi:http://dx.doi.org/10.1021/bi902018y
- ↑ Huddleston JP, Raushel FM. Biosynthesis of GDP-d-glycero-alpha-d-manno-heptose for the Capsular Polysaccharide of Campylobacter jejuni. Biochemistry. 2019 Sep 17;58(37):3893-3902. doi: 10.1021/acs.biochem.9b00548. , Epub 2019 Aug 29. PMID:31449400 doi:http://dx.doi.org/10.1021/acs.biochem.9b00548
- ↑ Nguyen HH, Wang L, Huang H, Peisach E, Dunaway-Mariano D, Allen KN. Structural Determinants of Substrate Recognition in the HAD Superfamily Member d-glycero-d-manno-Heptose-1,7-bisphosphate Phosphatase (GmhB) . Biochemistry. 2010 Jan 22. PMID:20050614 doi:10.1021/bi902019q
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