3n6q: Difference between revisions

Latest revision as of 09:09, 6 September 2023

Crystal structure of YghZ from E. coli

Structural highlights

3n6q is a 8 chain structure with sequence from Escherichia coli DH5alpha. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GPR_ECOLI Catalyzes the stereospecific, NADPH-dependent reduction of L-glyceraldehyde 3-phosphate (L-GAP). The physiological role of gpr is the detoxification of L-GAP, which may be formed by non-enzymatic racemization of GAP. Also involved in the stress response as a methylglyoxal reductase which converts the toxic metabolite methylglyoxal to acetol in vitro and in vivo.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Structural biology and structural genomics projects routinely rely on recombinantly expressed proteins, but many proteins and complexes are difficult to obtain by this approach. We investigated native source proteins for high-throughput protein crystallography applications. The Escherichia coli proteome was fractionated, purified, crystallized, and structurally characterized. Macro-scale fermentation and fractionation were used to subdivide the soluble proteome into 408 unique fractions of which 295 fractions yielded crystals in microfluidic crystallization chips. Of the 295 crystals, 152 were selected for optimization, diffraction screening, and data collection. Twenty-three structures were determined, four of which were novel. This study demonstrates the utility of native source proteins for high-throughput crystallography.

Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization.,Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T PLoS One. 2012;7(2):e32498. Epub 2012 Feb 29. PMID:22393408^[4]

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

References

↑ Grant AW, Steel G, Waugh H, Ellis EM. A novel aldo-keto reductase from Escherichia coli can increase resistance to methylglyoxal toxicity. FEMS Microbiol Lett. 2003 Jan 21;218(1):93-9. PMID:12583903
↑ Ko J, Kim I, Yoo S, Min B, Kim K, Park C. Conversion of methylglyoxal to acetol by Escherichia coli aldo-keto reductases. J Bacteriol. 2005 Aug;187(16):5782-9. PMID:16077126 doi:https://dx.doi.org/10.1128/JB.187.16.5782-5789.2005
↑ Desai KK, Miller BG. A metabolic bypass of the triosephosphate isomerase reaction. Biochemistry. 2008 Aug 5;47(31):7983-5. doi: 10.1021/bi801054v. Epub 2008 Jul 12. PMID:18620424 doi:https://dx.doi.org/10.1021/bi801054v
↑ Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T. Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization. PLoS One. 2012;7(2):e32498. Epub 2012 Feb 29. PMID:22393408 doi:10.1371/journal.pone.0032498

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OCA

[1] Grant AW, Steel G, Waugh H, Ellis EM. A novel aldo-keto reductase from Escherichia coli can increase resistance to methylglyoxal toxicity. FEMS Microbiol Lett. 2003 Jan 21;218(1):93-9. PMID:12583903

[2] Ko J, Kim I, Yoo S, Min B, Kim K, Park C. Conversion of methylglyoxal to acetol by Escherichia coli aldo-keto reductases. J Bacteriol. 2005 Aug;187(16):5782-9. PMID:16077126 doi:https://dx.doi.org/10.1128/JB.187.16.5782-5789.2005

[3] Desai KK, Miller BG. A metabolic bypass of the triosephosphate isomerase reaction. Biochemistry. 2008 Aug 5;47(31):7983-5. doi: 10.1021/bi801054v. Epub 2008 Jul 12. PMID:18620424 doi:https://dx.doi.org/10.1021/bi801054v

[4] Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T. Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization. PLoS One. 2012;7(2):e32498. Epub 2012 Feb 29. PMID:22393408 doi:10.1371/journal.pone.0032498

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@@ Line 3: / Line 3: @@
 <StructureSection load='3n6q' size='340' side='right'caption='[[3n6q]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3n6q]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N6Q FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3n6q]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH5alpha Escherichia coli DH5alpha]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N6Q FirstGlance]. <br>
-</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></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]] 1.8&#8491;</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></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=3n6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n6q OCA], [https://pdbe.org/3n6q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n6q RCSB], [https://www.ebi.ac.uk/pdbsum/3n6q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n6q ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/GPR_ECOLI GPR_ECOLI]] Catalyzes the stereospecific, NADPH-dependent reduction of L-glyceraldehyde 3-phosphate (L-GAP). The physiological role of gpr is the detoxification of L-GAP, which may be formed by non-enzymatic racemization of GAP. Also involved in the stress response as a methylglyoxal reductase which converts the toxic metabolite methylglyoxal to acetol in vitro and in vivo.<ref>PMID:12583903</ref> <ref>PMID:16077126</ref> <ref>PMID:18620424</ref>
+[https://www.uniprot.org/uniprot/GPR_ECOLI GPR_ECOLI] Catalyzes the stereospecific, NADPH-dependent reduction of L-glyceraldehyde 3-phosphate (L-GAP). The physiological role of gpr is the detoxification of L-GAP, which may be formed by non-enzymatic racemization of GAP. Also involved in the stress response as a methylglyoxal reductase which converts the toxic metabolite methylglyoxal to acetol in vitro and in vivo.<ref>PMID:12583903</ref> <ref>PMID:16077126</ref> <ref>PMID:18620424</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Alber, T]]
+[[Category: Alber T]]
-[[Category: Echols, N]]
+[[Category: Echols N]]
-[[Category: May, A]]
+[[Category: May A]]
-[[Category: Totir, M]]
+[[Category: Totir M]]
-[[Category: Zubieta, C]]
+[[Category: Zubieta C]]
-[[Category: Oxidoreductase]]
-[[Category: Tim barrel]]

3n6q: Difference between revisions

Latest revision as of 09:09, 6 September 2023

Crystal structure of YghZ from E. coli

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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