3l1v: Difference between revisions

Latest revision as of 08:28, 6 September 2023

Crystal structure of GmhB from E. coli in complex with calcium and phosphate.

Structural highlights

3l1v is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.954Å
Ligands:	CA, PO4, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

Lipopolysaccharide is a major component of the outer membrane of gram-negative bacteria and provides a permeability barrier to many commonly used antibiotics. ADP-heptose residues are an integral part of the LPS inner core, and mutants deficient in heptose biosynthesis demonstrate increased membrane permeability. The heptose biosynthesis pathway involves phosphorylation and dephosphorylation steps not found in other pathways for the synthesis of nucleotide sugar precursors. Consequently, the heptose biosynthetic pathway has been marked as a novel target for antibiotic adjuvants, which are compounds that facilitate and potentiate antibiotic activity. D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) catalyzes the third essential step of LPS heptose biosynthesis. This study describes the first crystal structure of GmhB and enzymatic analysis of the protein. Structure-guided mutations followed by steady state kinetic analysis, together with established precedent for HAD phosphatases, suggest that GmhB functions through a phosphoaspartate intermediate. This study provides insight into the structure-function relationship of GmhB, a new target for combatting gram-negative bacterial infection.

Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli.,Taylor PL, Sugiman-Marangos S, Zhang K, Valvano MA, Wright GD, Junop MS Biochemistry. 2010 Feb 9;49(5):1033-41. PMID:20050699^[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:https://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:https://dx.doi.org/10.1021/acs.biochem.9b00548
↑ Taylor PL, Sugiman-Marangos S, Zhang K, Valvano MA, Wright GD, Junop MS. Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli. Biochemistry. 2010 Feb 9;49(5):1033-41. PMID:20050699 doi:10.1021/bi901780j

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] 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

[3] 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:https://dx.doi.org/10.1021/bi902018y

[4] 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:https://dx.doi.org/10.1021/acs.biochem.9b00548

[5] Taylor PL, Sugiman-Marangos S, Zhang K, Valvano MA, Wright GD, Junop MS. Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli. Biochemistry. 2010 Feb 9;49(5):1033-41. PMID:20050699 doi:10.1021/bi901780j

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[2]

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[4]

[5]

@@ Line 1: / Line 1: @@
 ==Crystal structure of GmhB from E. coli in complex with calcium and phosphate.==
-<StructureSection load='3l1v' size='340' side='right' caption='[[3l1v]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='3l1v' size='340' side='right'caption='[[3l1v]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3l1v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L1V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3l1v]] is a 2 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=3L1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L1V FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.954&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3l1u|3l1u]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=83333 ECOLI])</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=3l1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1v OCA], [https://pdbe.org/3l1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l1v RCSB], [https://www.ebi.ac.uk/pdbsum/3l1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l1v 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=3l1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1v OCA], [http://pdbe.org/3l1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l1v RCSB], [http://www.ebi.ac.uk/pdbsum/3l1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3l1v ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GMHB_ECOLI GMHB_ECOLI]] Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate intermediate into D-glycero-beta-D-manno-heptose 1-phosphate (HBP) by removing the phosphate group at the C-7 position. Also catalyzes the dephosphorylation of fructose-1,6-bisphosphate (Fru1,6bisP).<ref>PMID:11751812</ref> <ref>PMID:16990279</ref>
+[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/3l1v_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/3l1v_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Junop, M S]]
+[[Category: Large Structures]]
-[[Category: Sugiman-Marangos, S N]]
+[[Category: Junop MS]]
-[[Category: Carbohydrate metabolism]]
+[[Category: Sugiman-Marangos SN]]
-[[Category: Heptose]]
-[[Category: Hydrolase]]
-[[Category: Lipopolysaccharide biosynthesis]]
-[[Category: Lps biosynthesis]]
-[[Category: Sugar phosphatase]]

3l1v: Difference between revisions

Latest revision as of 08:28, 6 September 2023

Crystal structure of GmhB from E. coli in complex with calcium and phosphate.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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