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1yi1

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Crystal structure of Arabidopsis thaliana Acetohydroxyacid synthase In Complex With A Sulfonylurea Herbicide, Tribenuron methyl

Structural highlights

1yi1 is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ILVB_ARATH Catalyzes the formation of acetolactate from pyruvate, the first step in valine and isoleucine biosynthesis.^[1] ^[2] [:]^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The sulfonylureas and imidazolinones are potent commercial herbicide families. They are among the most popular choices for farmers worldwide, because they are nontoxic to animals and highly selective. These herbicides inhibit branched-chain amino acid biosynthesis in plants by targeting acetohydroxyacid synthase (AHAS, EC 2.2.1.6). This report describes the 3D structure of Arabidopsis thaliana AHAS in complex with five sulfonylureas (to 2.5 A resolution) and with the imidazolinone, imazaquin (IQ; 2.8 A). Neither class of molecule has a structure that mimics the substrates for the enzyme, but both inhibit by blocking a channel through which access to the active site is gained. The sulfonylureas approach within 5 A of the catalytic center, which is the C2 atom of the cofactor thiamin diphosphate, whereas IQ is at least 7 A from this atom. Ten of the amino acid residues that bind the sulfonylureas also bind IQ. Six additional residues interact only with the sulfonylureas, whereas there are two residues that bind IQ but not the sulfonylureas. Thus, the two classes of inhibitor occupy partially overlapping sites but adopt different modes of binding. The increasing emergence of resistant weeds due to the appearance of mutations that interfere with the inhibition of AHAS is now a worldwide problem. The structures described here provide a rational molecular basis for understanding these mutations, thus allowing more sophisticated AHAS inhibitors to be developed. There is no previously described structure for any plant protein in complex with a commercial herbicide.

Herbicide-binding sites revealed in the structure of plant acetohydroxyacid synthase.,McCourt JA, Pang SS, King-Scott J, Guddat LW, Duggleby RG Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):569-73. Epub 2006 Jan 10. PMID:16407096^[9]

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

References

↑ Mazur BJ, Chui CF, Smith JK. Isolation and characterization of plant genes coding for acetolactate synthase, the target enzyme for two classes of herbicides. Plant Physiol. 1987 Dec;85(4):1110-7. PMID:16665813
↑ Sathasivan K, Haughn GW, Murai N. Nucleotide sequence of a mutant acetolactate synthase gene from an imidazolinone-resistant Arabidopsis thaliana var. Columbia. Nucleic Acids Res. 1990 Apr 25;18(8):2188. PMID:2336405
↑ Haughn GW, Somerville CR. A Mutation Causing Imidazolinone Resistance Maps to the Csr1 Locus of Arabidopsis thaliana. Plant Physiol. 1990 Apr;92(4):1081-5. PMID:16667374
↑ Sathasivan K, Haughn GW, Murai N. Molecular Basis of Imidazolinone Herbicide Resistance in Arabidopsis thaliana var Columbia. Plant Physiol. 1991 Nov;97(3):1044-50. PMID:16668488
↑ Ott KH, Kwagh JG, Stockton GW, Sidorov V, Kakefuda G. Rational molecular design and genetic engineering of herbicide resistant crops by structure modeling and site-directed mutagenesis of acetohydroxyacid synthase. J Mol Biol. 1996 Oct 25;263(2):359-68. PMID:8913312 doi:http://dx.doi.org/10.1006/jmbi.1996.0580
↑ Chang AK, Duggleby RG. Expression, purification and characterization of Arabidopsis thaliana acetohydroxyacid synthase. Biochem J. 1997 Oct 1;327 ( Pt 1):161-9. PMID:9355748
↑ Chang AK, Duggleby RG. Herbicide-resistant forms of Arabidopsis thaliana acetohydroxyacid synthase: characterization of the catalytic properties and sensitivity to inhibitors of four defined mutants. Biochem J. 1998 Aug 1;333 ( Pt 3):765-77. PMID:9677339
↑ Lee YT, Chang AK, Duggleby RG. Effect of mutagenesis at serine 653 of Arabidopsis thaliana acetohydroxyacid synthase on the sensitivity to imidazolinone and sulfonylurea herbicides. FEBS Lett. 1999 Jun 11;452(3):341-5. PMID:10386618
↑ McCourt JA, Pang SS, King-Scott J, Guddat LW, Duggleby RG. Herbicide-binding sites revealed in the structure of plant acetohydroxyacid synthase. Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):569-73. Epub 2006 Jan 10. PMID:16407096

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yi1"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Arabidopsis thaliana Acetohydroxyacid synthase In Complex With A Sulfonylurea Herbicide, Tribenuron methyl==
-<StructureSection load='1yi1' size='340' side='right' caption='[[1yi1]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='1yi1' size='340' side='right'caption='[[1yi1]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yi1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YI1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yi1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YI1 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1TB:METHYL+2-[4-METHOXY-6-METHYL-1,3,5-TRAZIN-2-YL(METHYL)CARBAMOYLSULFAMOYL]BENZOATE'>1TB</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene>, <scene name='pdbligand=P22:ETHYL+DIHYDROGEN+DIPHOSPHATE'>P22</scene><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]] 2.9&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1TB:METHYL+2-[4-METHOXY-6-METHYL-1,3,5-TRAZIN-2-YL(METHYL)CARBAMOYLSULFAMOYL]BENZOATE'>1TB</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene>, <scene name='pdbligand=P22:ETHYL+DIHYDROGEN+DIPHOSPHATE'>P22</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jsc|1jsc]], [[1n0h|1n0h]], [[1t9b|1t9b]], [[1t9a|1t9a]], [[1t9c|1t9c]], [[1t9d|1t9d]], [[1yhy|1yhy]], [[1yhz|1yhz]], [[1yi0|1yi0]]</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=1yi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yi1 OCA], [https://pdbe.org/1yi1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yi1 RCSB], [https://www.ebi.ac.uk/pdbsum/1yi1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yi1 ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ILVB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
+</table>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetolactate_synthase Acetolactate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.6 2.2.1.6] </span></td></tr>
+== Function ==
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yi1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yi1 RCSB], [http://www.ebi.ac.uk/pdbsum/1yi1 PDBsum]</span></td></tr>
+[https://www.uniprot.org/uniprot/ILVB_ARATH ILVB_ARATH] Catalyzes the formation of acetolactate from pyruvate, the first step in valine and isoleucine biosynthesis.<ref>PMID:16665813</ref> <ref>PMID:2336405</ref> [:]<ref>PMID:16667374</ref> <ref>PMID:16668488</ref> <ref>PMID:8913312</ref> <ref>PMID:9355748</ref> <ref>PMID:9677339</ref> <ref>PMID:10386618</ref>
-<table>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yi/1yi1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yi/1yi1_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yi1 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1yi1" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Acetolactate synthase]]
 [[Category: Arabidopsis thaliana]]
-[[Category: Duggleby, R G.]]
+[[Category: Large Structures]]
-[[Category: Guddat, L W.]]
+[[Category: Duggleby RG]]
-[[Category: King-Scott, J.]]
+[[Category: Guddat LW]]
-[[Category: McCourt, J A.]]
+[[Category: King-Scott J]]
-[[Category: Pang, S S.]]
+[[Category: McCourt JA]]
-[[Category: Acetohydroxyacid synthase]]
+[[Category: Pang SS]]
-[[Category: Acetolactate synthase]]
-[[Category: Ch]]
-[[Category: Cysteine-s-dioxide]]
-[[Category: Fad]]
-[[Category: Herbicide]]
-[[Category: Inhibitor]]
-[[Category: Sulfonylurea]]
-[[Category: Thiamin diphosphate]]
-[[Category: Transferase]]
-[[Category: Tribenuron methyl]]

1yi1

From Proteopedia

Current revision

Crystal structure of Arabidopsis thaliana Acetohydroxyacid synthase In Complex With A Sulfonylurea Herbicide, Tribenuron methyl

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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