4w7h: Difference between revisions
New page: '''Unreleased structure''' The entry 4w7h is ON HOLD Authors: Takase, R., Mikami, B., Kawai, S., Murata, K., Hashimoto, W. Description: Crystal structure of coenzyme requirement-altere... |
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The | ==Crystal Structure of DEH Reductase A1-R Mutant== | ||
<StructureSection load='4w7h' size='340' side='right'caption='[[4w7h]], [[Resolution|resolution]] 3.11Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4w7h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W7H FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.11Å</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=4w7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7h OCA], [https://pdbe.org/4w7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w7h RCSB], [https://www.ebi.ac.uk/pdbsum/4w7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7h ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/D6RU56_9SPHN D6RU56_9SPHN] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The alginate-assimilating bacterium, Sphingomonas sp. strain A1, degrades the polysaccharides to monosaccharides through four alginate lyase reactions. The resultant monosaccharide, which is nonenzymatically converted to 4-deoxy-l-erythro-5-hexoseulose uronate (DEH), is further metabolized to 2-keto-3-deoxy-d-gluconate by NADPH-dependent reductase A1-R in the short-chain dehydrogenase/reductase (SDR) family. A1-R-deficient cells produced another DEH reductase, designated A1-R', with a preference for NADH. Here, we show the identification of a novel NADH-dependent DEH reductase A1-R' in strain A1, structural determination of A1-R' by x-ray crystallography, and structure-based conversion of a coenzyme requirement in SDR enzymes, A1-R and A1-R'. A1-R' was purified from strain A1 cells and enzymatically characterized. Except for the coenzyme requirement, there was no significant difference in enzyme characteristics between A1-R and A1-R'. Crystal structures of A1-R' and A1-R'.NAD(+) complex were determined at 1.8 and 2.7 A resolutions, respectively. Because of a 64% sequence identity, overall structures of A1-R' and A1-R were similar, although a difference in the coenzyme-binding site (particularly the nucleoside ribose 2' region) was observed. Distinct from A1-R, A1-R' included a negatively charged, shallower binding site. These differences were caused by amino acid residues on the two loops around the site. The A1-R' mutant with the two A1-R-typed loops maintained potent enzyme activity with specificity for NADPH rather than NADH, demonstrating that the two loops determine the coenzyme requirement, and loop exchange is a promising method for conversion of coenzyme requirement in the SDR family. | |||
Structure-based Conversion of the Coenzyme Requirement of a Short-chain Dehydrogenase/Reductase Involved in Bacterial Alginate Metabolism.,Takase R, Mikami B, Kawai S, Murata K, Hashimoto W J Biol Chem. 2014 Nov 28;289(48):33198-214. doi: 10.1074/jbc.M114.585661. Epub, 2014 Oct 6. PMID:25288804<ref>PMID:25288804</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4w7h" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Carbonyl reductase 3D structures|Carbonyl reductase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Sphingomonas sp. A1]] | |||
[[Category: Hashimoto W]] | |||
[[Category: Kawai S]] | |||
[[Category: Mikami B]] | |||
[[Category: Murata K]] | |||
[[Category: Takase R]] | |||
Latest revision as of 18:21, 8 November 2023
Crystal Structure of DEH Reductase A1-R MutantCrystal Structure of DEH Reductase A1-R Mutant
Structural highlights
FunctionPublication Abstract from PubMedThe alginate-assimilating bacterium, Sphingomonas sp. strain A1, degrades the polysaccharides to monosaccharides through four alginate lyase reactions. The resultant monosaccharide, which is nonenzymatically converted to 4-deoxy-l-erythro-5-hexoseulose uronate (DEH), is further metabolized to 2-keto-3-deoxy-d-gluconate by NADPH-dependent reductase A1-R in the short-chain dehydrogenase/reductase (SDR) family. A1-R-deficient cells produced another DEH reductase, designated A1-R', with a preference for NADH. Here, we show the identification of a novel NADH-dependent DEH reductase A1-R' in strain A1, structural determination of A1-R' by x-ray crystallography, and structure-based conversion of a coenzyme requirement in SDR enzymes, A1-R and A1-R'. A1-R' was purified from strain A1 cells and enzymatically characterized. Except for the coenzyme requirement, there was no significant difference in enzyme characteristics between A1-R and A1-R'. Crystal structures of A1-R' and A1-R'.NAD(+) complex were determined at 1.8 and 2.7 A resolutions, respectively. Because of a 64% sequence identity, overall structures of A1-R' and A1-R were similar, although a difference in the coenzyme-binding site (particularly the nucleoside ribose 2' region) was observed. Distinct from A1-R, A1-R' included a negatively charged, shallower binding site. These differences were caused by amino acid residues on the two loops around the site. The A1-R' mutant with the two A1-R-typed loops maintained potent enzyme activity with specificity for NADPH rather than NADH, demonstrating that the two loops determine the coenzyme requirement, and loop exchange is a promising method for conversion of coenzyme requirement in the SDR family. Structure-based Conversion of the Coenzyme Requirement of a Short-chain Dehydrogenase/Reductase Involved in Bacterial Alginate Metabolism.,Takase R, Mikami B, Kawai S, Murata K, Hashimoto W J Biol Chem. 2014 Nov 28;289(48):33198-214. doi: 10.1074/jbc.M114.585661. Epub, 2014 Oct 6. PMID:25288804[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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