7bu3: Difference between revisions

Latest revision as of 15:33, 29 November 2023

Structure of alcohol dehydrogenase YjgB in complex with NADP from Escherichia coli

Structural highlights

7bu3 is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	ASP, GOL, NAP, PEG, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AHR_ECOLI Catalyzes the reduction of a wide range of aldehydes including aliphatic fatty aldehydes (C4-C16), into their corresponding alcohols. Has a strong preference for NADPH over NADH as the electron donor. Cannot use glyceraldehyde or a ketone as substrate. Is a relevant source of NADPH-dependent aldehyde reductase activity in E.coli. The in vivo functions of Ahr has yet to be determined.^[1] ^[2] ^[3]

Publication Abstract from PubMed

In metabolic engineering and synthetic biology fields, there have been efforts to produce variable bioalcohol fuels, such as isobutanol and 2-phenylethanol, in order to meet industrial demands. YjgB is an aldehyde dehydrogenase from Escherichia coli that shows nicotinamide adenine dinucleotide phosphate (NADP)-dependent broad selectivity for aldehyde derivatives with an aromatic ring or small aliphatic chain. This could contribute to the design of industrial synthetic pathways. We determined the crystal structures of YjgB for both its apo-form and NADP-complexed form at resolutions of 1.55 and 2.00 A, respectively, in order to understand the mechanism of broad substrate selectivity. The hydrophobic pocket of the active site and the nicotinamide ring of NADP(H) are both involved in conferring its broad specificity toward aldehyde substrates. In addition, based on docking-simulation data, we inferred that pi-pi stacking between substrates and aromatic side chains might play a crucial role in recognizing substrates. Our structural analysis of YjgB might provide insights into establishing frameworks to understand its broad substrate specificity and develop engineered enzymes for industrial biofuel synthesis.

Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli.,Nguyen GT, Kim YG, Ahn JW, Chang JH Molecules. 2020 May 21;25(10). pii: molecules25102404. doi:, 10.3390/molecules25102404. PMID:32455802^[4]

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

References

↑ Rodriguez GM, Atsumi S. Isobutyraldehyde production from Escherichia coli by removing aldehyde reductase activity. Microb Cell Fact. 2012 Jun 25;11:90. PMID:22731523 doi:10.1186/1475-2859-11-90
↑ Pick A, Rühmann B, Schmid J, Sieber V. Novel CAD-like enzymes from Escherichia coli K-12 as additional tools in chemical production. Appl Microbiol Biotechnol. 2013 Jul;97(13):5815-24. PMID:23093176 doi:10.1007/s00253-012-4474-5
↑ Akhtar MK, Turner NJ, Jones PR. Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):87-92. doi: 10.1073/pnas.1216516110. , Epub 2012 Dec 17. PMID:23248280 doi:https://dx.doi.org/10.1073/pnas.1216516110
↑ Nguyen GT, Kim YG, Ahn JW, Chang JH. Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli. Molecules. 2020 May 21;25(10). pii: molecules25102404. doi:, 10.3390/molecules25102404. PMID:32455802 doi:https://dx.doi.org/10.3390/molecules25102404

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OCA

[1] Rodriguez GM, Atsumi S. Isobutyraldehyde production from Escherichia coli by removing aldehyde reductase activity. Microb Cell Fact. 2012 Jun 25;11:90. PMID:22731523 doi:10.1186/1475-2859-11-90

[2] Pick A, Rühmann B, Schmid J, Sieber V. Novel CAD-like enzymes from Escherichia coli K-12 as additional tools in chemical production. Appl Microbiol Biotechnol. 2013 Jul;97(13):5815-24. PMID:23093176 doi:10.1007/s00253-012-4474-5

[3] Akhtar MK, Turner NJ, Jones PR. Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):87-92. doi: 10.1073/pnas.1216516110. , Epub 2012 Dec 17. PMID:23248280 doi:https://dx.doi.org/10.1073/pnas.1216516110

[4] Nguyen GT, Kim YG, Ahn JW, Chang JH. Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli. Molecules. 2020 May 21;25(10). pii: molecules25102404. doi:, 10.3390/molecules25102404. PMID:32455802 doi:https://dx.doi.org/10.3390/molecules25102404

[1]

[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='7bu3' size='340' side='right'caption='[[7bu3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7bu3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BU3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BU3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7bu3]] is a 2 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=7BU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BU3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ahr, AWG90_000500, B9M99_17975, B9T59_09540, C6B13_12130, CDC27_23140, D2188_25420, D3P01_20900, D9G11_20970, D9I87_13335, DND16_13855, DNQ45_13310, DU321_18055, E0L12_15935, ECONIH1_25310, ELV08_20515, EQ830_17095, EXX23_18790, EXX53_16635, FNJ83_00500, FV293_01340, MS6198_49940 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yjgB, ahr, A9P13_23120, A9X72_22295, AC789_1c46870, AM446_24685, AM464_15880, AUQ13_10955, AWP75_26740, BE963_12920, BON76_03580, BON87_21450, BvCms2454_04261, BvCmsKKP061_04826, BvCmsKSP011_04570, BvCmsKSP024_01161, BvCmsKSP045_03147, BvCmsKSP067_02166, BvCmsNSP047_01920, CRX46_16815, D9J60_11645, DJ503_08680, DS732_03420, DU309_23350, EC3234A_79c00790, ERS085365_04790, ERS085374_04180, ERS085416_04717, ERS139211_04850, EYY27_20520, FNJ69_20595, NCTC8959_04532, NCTC9050_02355, NCTC9077_05531, NCTC9117_05474, PGD_03453, SAMEA3472056_04737, WR15_06500, YDC107_2991 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase_(NADP(+)) Alcohol dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.2 1.1.1.2] </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=7bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bu3 OCA], [https://pdbe.org/7bu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bu3 RCSB], [https://www.ebi.ac.uk/pdbsum/7bu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bu3 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7bu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bu3 OCA], [http://pdbe.org/7bu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bu3 RCSB], [http://www.ebi.ac.uk/pdbsum/7bu3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bu3 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AHR_ECOLI AHR_ECOLI] Catalyzes the reduction of a wide range of aldehydes including aliphatic fatty aldehydes (C4-C16), into their corresponding alcohols. Has a strong preference for NADPH over NADH as the electron donor. Cannot use glyceraldehyde or a ketone as substrate. Is a relevant source of NADPH-dependent aldehyde reductase activity in E.coli. The in vivo functions of Ahr has yet to be determined.<ref>PMID:22731523</ref> <ref>PMID:23093176</ref> <ref>PMID:23248280</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Ahn, J W]]
+[[Category: Ahn J-W]]
-[[Category: Chang, J H]]
+[[Category: Chang JH]]
-[[Category: Kim, Y G]]
+[[Category: Kim Y-G]]
-[[Category: Nguyen, G T]]
+[[Category: Nguyen GT]]
-[[Category: Alcohol dehydrogenase]]
-[[Category: Oxidoreductase]]

7bu3: Difference between revisions

Latest revision as of 15:33, 29 November 2023

Structure of alcohol dehydrogenase YjgB in complex with NADP from Escherichia coli

Structural highlights

Function

Publication Abstract from PubMed

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References

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