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7c5q

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Crystal Structure of H177A mutant Glyceraldehyde-3-phosphate dehydrogenase1 from Escherichia coli complexed with BPG at 2.13 Angstrom resolution

Structural highlights

7c5q is a 4 chain structure with sequence from Escherichia coli BL21(DE3). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.13Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A140NCK4_ECOBD Catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG.[ARBA:ARBA00003501]

Publication Abstract from PubMed

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a highly conserved enzyme involved in the ubiquitous process of glycolysis and presents a loop (residues 208-215 of Escherichia coli GAPDH) in two alternative conformations (I and II). It is uncertain what triggers this loop rearrangement, as well as which is the precise site from which phosphate attacks the thioacyl intermediate precursor of 1,3-bisphosphoglycerate (BPG). To clarify these uncertainties, we determined the crystal structures of complexes of wild-type GAPDH (WT) with NAD and phosphate or G3P, and of essentially inactive GAPDH mutants (C150S, H177A), trapping crystal structures for the thioacyl intermediate or for ternary complexes with NAD and either phosphate, BPG, or G3P. Analysis of these structures reported here lead us to propose that phosphate is located in the "new Pi site" attacks the thioester bond of the thioacyl intermediate to generate 1,3-bisphosphoglyceric acid (BPG). In the structure of the thioacyl intermediate, the mobile loop is in conformation II in subunits O, P, and R, while both conformations coexist in subunit Q. Moreover, only the Q subunit hosts bound NADH. In the R subunit, only the pyrophosphate part of NADH is well defined, and NADH is totally absent from the O and P subunits. Thus, the change in loop conformation appears to occur after NADH is produced, before NADH is released. In addition, two new D-glyceraldehyde-3-phosphate (G3P) binding forms are observed in WT.NAD.G3P and C150A+H177A.NAD.G3P. In summary, this paper improves our understanding of the GAPDH catalytic mechanism, particularly regarding BPG formation.

Novel Structures of Type 1 Glyceraldehyde-3-phosphate Dehydrogenase from Escherichia coli Provide New Insights into the Mechanism of Generation of 1,3-Bisphosphoglyceric Acid.,Zhang L, Liu M, Bao L, Bostrom KI, Yao Y, Li J, Gu S, Ji C Biomolecules. 2021 Oct 22;11(11). pii: biom11111565. doi: 10.3390/biom11111565. PMID:34827563^[1]

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

References

↑ Zhang L, Liu M, Bao L, Bostrom KI, Yao Y, Li J, Gu S, Ji C. Novel Structures of Type 1 Glyceraldehyde-3-phosphate Dehydrogenase from Escherichia coli Provide New Insights into the Mechanism of Generation of 1,3-Bisphosphoglyceric Acid. Biomolecules. 2021 Oct 22;11(11). pii: biom11111565. doi: 10.3390/biom11111565. PMID:34827563 doi:http://dx.doi.org/10.3390/biom11111565

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7c5q"

@@ Line 3: / Line 3: @@
 <StructureSection load='7c5q' size='340' side='right'caption='[[7c5q]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7c5q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C5Q FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7c5q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C5Q FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DG4:phosphono+(2S)-2-oxidanyl-3-phosphonooxy-propanoate'>DG4</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G3H:GLYCERALDEHYDE-3-PHOSPHATE'>G3H</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.13&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ECBD_2224 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=469008 ECOBD])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DG4:phosphono+(2S)-2-oxidanyl-3-phosphonooxy-propanoate'>DG4</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G3H:GLYCERALDEHYDE-3-PHOSPHATE'>G3H</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=7c5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c5q OCA], [https://pdbe.org/7c5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c5q RCSB], [https://www.ebi.ac.uk/pdbsum/7c5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c5q ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/A0A140NCK4_ECOBD A0A140NCK4_ECOBD]] Catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG.[ARBA:ARBA00003501]
+[https://www.uniprot.org/uniprot/A0A140NCK4_ECOBD A0A140NCK4_ECOBD] Catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG.[ARBA:ARBA00003501]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ecobd]]
 [[Category: Large Structures]]
-[[Category: Bao, L Y]]
+[[Category: Bao LY]]
-[[Category: Bostrom, I K]]
+[[Category: Bostrom IK]]
-[[Category: Chen, A Q]]
+[[Category: Chen AQ]]
-[[Category: Gu, S H]]
+[[Category: Gu SH]]
-[[Category: Ji, C N]]
+[[Category: Ji CN]]
-[[Category: Li, J X]]
+[[Category: Li JX]]
-[[Category: Liu, M R]]
+[[Category: Liu MR]]
-[[Category: Wang, Y D]]
+[[Category: Wang YD]]
-[[Category: Yao, Y C]]
+[[Category: Yao YC]]
-[[Category: Zhang, L]]
+[[Category: Zhang L]]
-[[Category: Ecgapdh 1]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]

7c5q

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Current revision

Crystal Structure of H177A mutant Glyceraldehyde-3-phosphate dehydrogenase1 from Escherichia coli complexed with BPG at 2.13 Angstrom resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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