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7p75

From Proteopedia

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Re-engineered 2-deoxy-D-ribose-5-phosphate aldolase catalysing asymmetric Michael addition reactions in substrate-free state

Structural highlights

7p75 is a 2 chain structure with sequence from Escherichia coli ATCC 8739. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.23Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DEOC_ECOLI Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.[HAMAP-Rule:MF_00592]

Publication Abstract from PubMed

Class I aldolases catalyze asymmetric aldol addition reactions and have found extensive application in the biocatalytic synthesis of chiral beta-hydroxy-carbonyl compounds. However, the usefulness of these powerful enzymes for application in other C-C bond-forming reactions remains thus far unexplored. The redesign of class I aldolases to expand their catalytic repertoire to include non-native carboligation reactions therefore continues to be a major challenge. Here, we report the successful redesign of 2-deoxy-d-ribose-5-phosphate aldolase (DERA) from Escherichia coli, an archetypical class I aldolase, to proficiently catalyze enantioselective Michael additions of nitromethane to alpha,beta-unsaturated aldehydes to yield various pharmaceutically relevant chiral synthons. After 11 rounds of directed evolution, the redesigned DERA enzyme (DERA-MA) carried 12 amino-acid substitutions and had an impressive 190-fold enhancement in catalytic activity compared to the wildtype enzyme. The high catalytic efficiency of DERA-MA for this abiological reaction makes it a proficient "Michaelase" with potential for biocatalytic application. Crystallographic analysis provides a structural context for the evolved activity. Whereas an aldolase acts naturally by activating the enzyme-bound substrate as a nucleophile (enamine-based mechanism), DERA-MA instead acts by activating the enzyme-bound substrate as an electrophile (iminium-based mechanism). This work demonstrates the power of directed evolution to expand the reaction scope of natural aldolases to include asymmetric Michael addition reactions and presents opportunities to explore iminium catalysis with DERA-derived catalysts inspired by developments in the organocatalysis field.

Unlocking Asymmetric Michael Additions in an Archetypical Class I Aldolase by Directed Evolution.,Kunzendorf A, Xu G, van der Velde JJH, Rozeboom HJ, Thunnissen AWH, Poelarends GJ ACS Catal. 2021 Nov 5;11(21):13236-13243. doi: 10.1021/acscatal.1c03911. Epub, 2021 Oct 15. PMID:34765282^[1]

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

References

↑ Kunzendorf A, Xu G, van der Velde JJH, Rozeboom HJ, Thunnissen AWH, Poelarends GJ. Unlocking Asymmetric Michael Additions in an Archetypical Class I Aldolase by Directed Evolution. ACS Catal. 2021 Nov 5;11(21):13236-13243. doi: 10.1021/acscatal.1c03911. Epub, 2021 Oct 15. PMID:34765282 doi:http://dx.doi.org/10.1021/acscatal.1c03911

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/7p75"

@@ Line 3: / Line 3: @@
 <StructureSection load='7p75' size='340' side='right'caption='[[7p75]], [[Resolution|resolution]] 1.23&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7p75]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P75 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P75 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7p75]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_ATCC_8739 Escherichia coli ATCC 8739]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P75 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P75 FirstGlance]. <br>
-</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] </span></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]] 1.23&#8491;</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=7p75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p75 OCA], [https://pdbe.org/7p75 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p75 RCSB], [https://www.ebi.ac.uk/pdbsum/7p75 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p75 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DEOC_ECOLC DEOC_ECOLC]] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
+[https://www.uniprot.org/uniprot/DEOC_ECOLI DEOC_ECOLI] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.[HAMAP-Rule:MF_00592]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 </div>
 <div class="pdbe-citations 7p75" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aldolase 3D structures|Aldolase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Deoxyribose-phosphate aldolase]]
+[[Category: Escherichia coli ATCC 8739]]
 [[Category: Large Structures]]
-[[Category: Kunzendorf, A]]
+[[Category: Kunzendorf A]]
-[[Category: Poelarends, G J]]
+[[Category: Poelarends GJ]]
-[[Category: Rozeboom, H J]]
+[[Category: Rozeboom HJ]]
-[[Category: Thunnissen, A M.W H]]
+[[Category: Thunnissen AMWH]]
-[[Category: Aldolase]]
-[[Category: Carboligase]]
-[[Category: Carbon-carbon lyase]]
-[[Category: Dera]]
-[[Category: Directed evolution]]
-[[Category: Lyase]]
-[[Category: Michael addition]]
-[[Category: Protein engineering]]

7p75

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Current revision

Re-engineered 2-deoxy-D-ribose-5-phosphate aldolase catalysing asymmetric Michael addition reactions in substrate-free state

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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