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5ucn

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Class II fructose-1,6-bisphosphate aldolase E142A variant of Helicobacter pylori with DHAP

Structural highlights

5ucn is a 2 chain structure with sequence from Helicobacter pylori 26695. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.67Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ALF_HELPY Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity).

Publication Abstract from PubMed

Crystal structures of two bacterial metal (Zn) dependent D-fructose 1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 A resolution. The ligand complexes cryotrapped in native or mutant H. pylori aldolase crystals enabled a novel mechanistic description of FBP C3-C4 bond cleavage. The reaction mechanism uses active site remodelling during the catalytic cycle implicating relocation of the Zn cofactor that is mediated by conformational changes of active site loops. Substrate binding initiates conformational changes, triggered upon P1-phosphate binding, which liberates the Zn chelating His180, allowing it to act as a general base for the proton abstraction at the FBP C4-hydroxyl group. A second zinc chelating His83 hydrogen bonds the substrate C4- hydroxyl group and assists cleavage by stabilizing the developing negative charge during proton abstraction. Cleavage is concerted with relocation of the metal cofactor from an interior to a surface exposed site, thereby stabilizing the nascent enediolate form. Conserved residue Glu142 is essential for protonation of the enediolate form, prior to product release. A D-tagatose 1,6-bisphosphate enzymatic complex reveals how His180 mediated proton abstraction controls stereospecificity of the cleavage reaction. Recognition and discrimination of the reaction products, dihydroxyacetone-P and D-glyceraldehyde-3-P, occurs via charged hydrogen bonds between hydroxyl groups of the triose-Ps and conserved residues, Asp82 and Asp255, respectively, and are crucial aspects of the enzyme's role in gluconeogenesis. Conformational changes in mobile loops beta5-alpha7 and beta6-alpha8 (containing catalytic residues Glu142 and His180, respectively) drive active site remodelling enabling the relocation of the metal cofactor.

Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.,Jacques B, Coincon M, Sygusch J J Biol Chem. 2018 Mar 28. pii: RA117.001098. doi: 10.1074/jbc.RA117.001098. PMID:29593097^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jacques B, Coincon M, Sygusch J. Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases. J Biol Chem. 2018 Mar 28. pii: RA117.001098. doi: 10.1074/jbc.RA117.001098. PMID:29593097 doi:http://dx.doi.org/10.1074/jbc.RA117.001098

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ucn"

Categories: Helicobacter pylori 26695 | Large Structures | Jacques B | Sygusch J

@@ Line 1: / Line 1: @@
 ==Class II fructose-1,6-bisphosphate aldolase E142A variant of Helicobacter pylori with DHAP==
-<StructureSection load='5ucn' size='340' side='right' caption='[[5ucn]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
+<StructureSection load='5ucn' size='340' side='right'caption='[[5ucn]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ucn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UCN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UCN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ucn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UCN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.67&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphate_aldolase Fructose-bisphosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.13 4.1.2.13] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5ucn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ucn OCA], [http://pdbe.org/5ucn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ucn RCSB], [http://www.ebi.ac.uk/pdbsum/5ucn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ucn ProSAT]</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=5ucn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ucn OCA], [https://pdbe.org/5ucn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ucn RCSB], [https://www.ebi.ac.uk/pdbsum/5ucn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ucn ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ALF_HELPY ALF_HELPY]] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity).
+[https://www.uniprot.org/uniprot/ALF_HELPY ALF_HELPY] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5ucn" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aldolase 3D structures|Aldolase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Fructose-bisphosphate aldolase]]
+[[Category: Helicobacter pylori 26695]]
-[[Category: Jacques, B]]
+[[Category: Large Structures]]
-[[Category: Sygusch, J]]
+[[Category: Jacques B]]
-[[Category: Glycolysis]]
+[[Category: Sygusch J]]
-[[Category: Lyase]]
-[[Category: Metalloenzyme]]

5ucn

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Current revision

Class II fructose-1,6-bisphosphate aldolase E142A variant of Helicobacter pylori with DHAP

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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