This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5hht

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of E. coli transketolase triple variant Ser385Tyr/Asp469Thr/Arg520Gln

Structural highlights

5hht 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 1.5Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TKT1_ECOLI Catalyzes the reversible transfer of a two-carbon ketol group from sedoheptulose-7-phosphate to glyceraldehyde-3-phosphate, producing xylulose-5-phosphate and ribose-5-phosphate. Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.^[1]

Publication Abstract from PubMed

The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting pi-pi stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies.

Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes.,Affaticati PE, Dai SB, Payongsri P, Hailes HC, Tittmann K, Dalby PA Sci Rep. 2016 Oct 21;6:35716. doi: 10.1038/srep35716. PMID:27767080^[2]

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

References

↑ Asztalos P, Parthier C, Golbik R, Kleinschmidt M, Hubner G, Weiss MS, Friedemann R, Wille G, Tittmann K. Strain and near attack conformers in enzymic thiamin catalysis: X-ray crystallographic snapshots of bacterial transketolase in covalent complex with donor ketoses xylulose 5-phosphate and fructose 6-phosphate, and in noncovalent complex with acceptor aldose ribose 5-phosphate. Biochemistry. 2007 Oct 30;46(43):12037-52. Epub 2007 Oct 3. PMID:17914867 doi:10.1021/bi700844m
↑ Affaticati PE, Dai SB, Payongsri P, Hailes HC, Tittmann K, Dalby PA. Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes. Sci Rep. 2016 Oct 21;6:35716. doi: 10.1038/srep35716. PMID:27767080 doi:http://dx.doi.org/10.1038/srep35716

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/5hht"

Categories: Escherichia coli K-12 | Large Structures | Dai S | Tittmann K

@@ Line 1: / Line 1: @@
 ==Crystal structure of E. coli transketolase triple variant Ser385Tyr/Asp469Thr/Arg520Gln==
-<StructureSection load='5hht' size='340' side='right' caption='[[5hht]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='5hht' size='340' side='right'caption='[[5hht]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5hht]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HHT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HHT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5hht]] 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=5HHT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HHT 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</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]] 1.5&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transketolase Transketolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.1 2.2.1.1] </span></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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=5hht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hht OCA], [http://pdbe.org/5hht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hht RCSB], [http://www.ebi.ac.uk/pdbsum/5hht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hht 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=5hht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hht OCA], [https://pdbe.org/5hht PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hht RCSB], [https://www.ebi.ac.uk/pdbsum/5hht PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hht ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TKT1_ECOLI TKT1_ECOLI]] Catalyzes the reversible transfer of a two-carbon ketol group from sedoheptulose-7-phosphate to glyceraldehyde-3-phosphate, producing xylulose-5-phosphate and ribose-5-phosphate. Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.<ref>PMID:17914867</ref>
+[https://www.uniprot.org/uniprot/TKT1_ECOLI TKT1_ECOLI] Catalyzes the reversible transfer of a two-carbon ketol group from sedoheptulose-7-phosphate to glyceraldehyde-3-phosphate, producing xylulose-5-phosphate and ribose-5-phosphate. Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.<ref>PMID:17914867</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5hht" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Transketolase 3D structures|Transketolase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Transketolase]]
+[[Category: Escherichia coli K-12]]
-[[Category: Dai, S]]
+[[Category: Large Structures]]
-[[Category: Tittmann, K]]
+[[Category: Dai S]]
-[[Category: Engineered variant]]
+[[Category: Tittmann K]]
-[[Category: Pentose phosphate pathway]]
-[[Category: Thiamin diphosphate]]
-[[Category: Transferase]]

5hht

From Proteopedia

Current revision

Crystal structure of E. coli transketolase triple variant Ser385Tyr/Asp469Thr/Arg520Gln

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox