5t79 - Revision history

OCA at 12:55, 4 October 2023

OCA — Wed, 04 Oct 2023 12:55:58 GMT

←Older revision		Revision as of 12:55, 4 October 2023
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	<StructureSection load='5t79' size='340' side='right'caption='[[5t79]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='5t79' size='340' side='right'caption='[[5t79]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t79]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Salty Salty~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T79 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5T79 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t79]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T79 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.86Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3erp\|3erp]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STM2406 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])~~</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=5t79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t79 OCA], [https://pdbe.org/5t79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t79 RCSB], [https://www.ebi.ac.uk/pdbsum/5t79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t79 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=5t79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t79 OCA], [~~http~~://pdbe.org/5t79 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t79 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t79 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t79 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8ZNA1_SALTY Q8ZNA1_SALTY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Salty~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-	[[Category: Anderson~~, W F~~]]	+	[[Category: Anderson WF]]
-	[[Category: Brunzelle~~, J S]]~~	+	[[Category: Brunzelle JS]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Evdokimova E]]
-	[[Category: Evdokimova, E]]	+	[[Category: Kudritska M]]
-	[[Category: Kudritska, M]]	+	[[Category: Savchenko A]]
-	[[Category: Savchenko, A]]	+	[[Category: Wawrzak Z]]
-	[[Category: Wawrzak, Z]]	+	[[Category: Yakunin AF]]
-	[[Category: Yakunin~~, A F]]~~	+
-	~~[[Category: Csgid]]~~	+
-	~~[[Category: Nadp-dependent oxidoreductase]]~~	+
-	~~[[Category: National institute of allergy and infectious disease]]~~	+
-	~~[[Category: Niaid]]~~	+
-	~~[[Category: Translation~~]]	+

OCA at 11:24, 16 September 2020

OCA — Wed, 16 Sep 2020 11:24:34 GMT

←Older revision		Revision as of 11:24, 16 September 2020
Line 1:		Line 1:

	==X-Ray Crystal Structure of a Novel Aldo-keto Reductases for the Biocatalytic Conversion of 3-hydroxybutanal to 1,3-butanediol==		==X-Ray Crystal Structure of a Novel Aldo-keto Reductases for the Biocatalytic Conversion of 3-hydroxybutanal to 1,3-butanediol==
-	<StructureSection load='5t79' size='340' side='right' caption='[[5t79]], [[Resolution\|resolution]] 1.86Å' scene=''>	+	<StructureSection load='5t79' size='340' side='right'caption='[[5t79]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t79]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T79 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T79 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t79]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T79 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T79 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3erp\|3erp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3erp\|3erp]]</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=5t79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t79 OCA], [http://pdbe.org/5t79 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t79 RCSB], [http://www.ebi.ac.uk/pdbsum/5t79 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t79 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STM2406 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=5t79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t79 OCA], [http://pdbe.org/5t79 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t79 RCSB], [http://www.ebi.ac.uk/pdbsum/5t79 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t79 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:

	==See Also==		==See Also==
-	*[[Aldo-keto reductase\|Aldo-keto reductase]]	+	*[[Aldo-keto reductase 3D structures\|Aldo-keto reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Salty]]
	[[Category: Anderson, W F]]		[[Category: Anderson, W F]]
	[[Category: Brunzelle, J S]]		[[Category: Brunzelle, J S]]

OCA at 17:45, 10 March 2017

OCA — Fri, 10 Mar 2017 17:45:20 GMT

←Older revision		Revision as of 17:45, 10 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5t79 is ~~ON HOLD until Paper~~ Publication	+	==X-Ray Crystal Structure of a Novel Aldo-keto Reductases for the Biocatalytic Conversion of 3-hydroxybutanal to 1,3-butanediol==
		+	<StructureSection load='5t79' size='340' side='right' caption='[[5t79]], [[Resolution\|resolution]] 1.86Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5t79]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T79 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T79 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3erp\|3erp]]</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=5t79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t79 OCA], [http://pdbe.org/5t79 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t79 RCSB], [http://www.ebi.ac.uk/pdbsum/5t79 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t79 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The non-natural alcohol 1,3-butanediol (1,3-BDO) is a valuable building block for the synthesis of various polymers. One of the potential pathways for the biosynthesis of 1,3-BDO includes the biotransformation of acetaldehyde to 1,3-BDO via 3-hydroxybutanal (3-HB) using aldolases and aldo-keto reductases. This pathway requires an aldo-keto reductase (AKR) selective for 3-HB, but inactive toward acetaldehyde, so it can be used for one pot synthesis. In this work, we screened over 20 purified uncharacterized AKRs for 3-HB reduction and identified 10 enzymes with significant activity and nine proteins with detectable activity. PA1127 from Pseudomonas aeruginosa showed the highest activity and was selected for comparative studies with STM2406 from Salmonella typhimurium, for which we have determined the crystal structure. Both AKRs used NADPH as cofactor, reduced a broad range of aldehydes, and showed low activity toward acetaldehyde. The crystal structures of STM2406 in complex with cacodylate or NADPH revealed the active site with bound molecules of a substrate mimic or cofactor. Site-directed mutagenesis of STM2406 and PA1127 identified the key residues important for activity against 3-HB and aromatic aldehydes, which include the residues of the substrate binding pocket and C-terminal loop. Our results revealed that the replacement of the STM2406 Asn65 by Met enhanced both activity and affinity of this protein toward 3-HB resulting in a seven-fold increase in kcat/Km Our work provided further insights into the molecular mechanisms of substrate selectivity of AKRs and rational design of these enzymes towards new substrates. IMPORTANCE: In this study, we identified several aldo-keto reductases with significant activity in the reduction of 3-hydroxybutanal to 1,3-BDO, an important commodity chemical. Biochemical and structural studies of these enzymes revealed the key catalytic and substrate binding residues including the two structural determinants necessary for high activity in the biosynthesis of 1,3-BDO. This work expands our understanding of the molecular mechanisms of substrate selectivity of AKRs and the potential for protein engineering of these enzymes for applications in the biocatalytic production of 1,3-BDO and other valuable chemicals.

-	~~Authors: Brunzelle~~, ~~J.S~~., ~~Wawrzak~~, Z., ~~Evdokimova~~, E., ~~Kudritska~~, M., ~~Savchenko~~, A., ~~Yakunin~~, A.F.~~, Anderson, W~~.F., ~~Center for Structural Genomics of Infectious Diseases (CSGID)~~	+	Structural and biochemical studies of novel aldo-keto reductases for the biocatalytic conversion of 3-hydroxybutanal to 1,3-butanediol.,Kim T, Flick R, Brunzelle J, Singer A, Evdokimova E, Brown G, Joo JC, Minasov GA, Anderson WF, Mahadevan R, Savchenko A, Yakunin AF Appl Environ Microbiol. 2017 Jan 27. pii: AEM.03172-16. doi:, 10.1128/AEM.03172-16. PMID:28130301<ref>PMID:28130301</ref>

-	~~Description: X-Ray Crystal Structure~~ of ~~a Novel Aldo-keto Reductases for~~ the ~~Biocatalytic Conversion~~ of 3-~~hydroxybutanal to 1,3~~-~~butanediol~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Wawrzak, Z]]~~	+	<div class="pdbe-citations 5t79" style="background-color:#fffaf0;"></div>
-	[[~~Category: Savchenko, A~~]]	+
-	[[Category: ~~Yakunin~~, A.F]]	+	==See Also==
-	[[Category: Brunzelle, J.S]]	+	*[[Aldo-keto reductase\|Aldo-keto reductase]]
-	[[Category: ~~Kudritska, M]]~~	+	== References ==
-	~~[[Category: Anderson, W.F]]~~	+	<references/>
-	~~[[Category: Center For~~ Structural ~~Genomics Of Infectious Diseases (Csgid)~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Anderson, W F]]
		+	[[Category: Brunzelle, J S]]
		+	[[Category: Structural genomic]]
	[[Category: Evdokimova, E]]		[[Category: Evdokimova, E]]
		+	[[Category: Kudritska, M]]
		+	[[Category: Savchenko, A]]
		+	[[Category: Wawrzak, Z]]
		+	[[Category: Yakunin, A F]]
		+	[[Category: Csgid]]
		+	[[Category: Nadp-dependent oxidoreductase]]
		+	[[Category: National institute of allergy and infectious disease]]
		+	[[Category: Niaid]]
		+	[[Category: Translation]]

OCA at 19:34, 22 December 2016

OCA — Thu, 22 Dec 2016 19:34:04 GMT

←Older revision		Revision as of 19:34, 22 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5t79 is ON HOLD	+	The entry 5t79 is ON HOLD until Paper Publication

	Authors: Brunzelle, J.S., Wawrzak, Z., Evdokimova, E., Kudritska, M., Savchenko, A., Yakunin, A.F., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)		Authors: Brunzelle, J.S., Wawrzak, Z., Evdokimova, E., Kudritska, M., Savchenko, A., Yakunin, A.F., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

OCA: Protected "5t79" [edit=sysop:move=sysop]

OCA — Wed, 14 Sep 2016 14:05:10 GMT

Protected "5t79" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:05, 14 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t79 is ON HOLD Authors: Brunzelle, J.S., Wawrzak, Z., Evdokimova, E., Kudritska, M., Savchenko, A., Yakunin, A.F., Anderson, W.F., Center for Struc...

OCA — Wed, 14 Sep 2016 14:05:09 GMT

New page: '''Unreleased structure''' The entry 5t79 is ON HOLD Authors: Brunzelle, J.S., Wawrzak, Z., Evdokimova, E., Kudritska, M., Savchenko, A., Yakunin, A.F., Anderson, W.F., Center for Struc...

New page

'''Unreleased structure'''

The entry 5t79 is ON HOLD

Authors: Brunzelle, J.S., Wawrzak, Z., Evdokimova, E., Kudritska, M., Savchenko, A., Yakunin, A.F., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Description: X-Ray Crystal Structure of a Novel Aldo-keto Reductases for the Biocatalytic Conversion of 3-hydroxybutanal to 1,3-butanediol
[[Category: Unreleased Structures]]
[[Category: Wawrzak, Z]]
[[Category: Savchenko, A]]
[[Category: Yakunin, A.F]]
[[Category: Brunzelle, J.S]]
[[Category: Kudritska, M]]
[[Category: Anderson, W.F]]
[[Category: Center For Structural Genomics Of Infectious Diseases (Csgid)]]
[[Category: Evdokimova, E]]