1iow

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[[Image:1iow.gif|left|200px]]
 
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{{Structure
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==COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE==
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|PDB= 1iow |SIZE=350|CAPTION= <scene name='initialview01'>1iow</scene>, resolution 1.9&Aring;
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<StructureSection load='1iow' size='340' side='right'caption='[[1iow]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE= <scene name='pdbsite=ADP:Adp+Binding+Site'>ADP</scene> and <scene name='pdbsite=LIG:Ligand+Binding+Site'>LIG</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene> and <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID'>PHY</scene>
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<table><tr><td colspan='2'>[[1iow]] is a 1 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IOW FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [https://pdbe.org/1iow PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [https://www.ebi.ac.uk/pdbsum/1iow PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iow ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DDLB_ECOLI DDLB_ECOLI] Cell wall formation.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/io/1iow_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1iow ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystallographic structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli complexed with a D-Ala-D-alpha-hydroxybutyrate phosphonate and the structure of the Y216F mutant ligase complexed with a D-Ala-D-Ala phosphinate have been determined to 2.2 and 1.9 A resolution, respectively, and refined to R factors of 0.156 and 0.158. In each complex the inhibitor has reacted with ATP to produce ADP and a tight-binding phosphorylated transition state intermediate. Comparison of these two structures with the known crystal structure of the phosphinate intermediate of the wild-type ligase shows no major conformational changes, but B factors indicate differences in mobility of loops covering the binding site. The weaker inhibition of the Y216F mutant by both inhibitors is thought to be due in part to the loss of an interloop hydrogen bond. A similar mechanism may account for poor inhibition of VanA, the homologous D-Ala:D-lactate ligase produced by vancomycin-resistant enterococci.
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'''COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE'''
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D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant.,Fan C, Park IS, Walsh CT, Knox JR Biochemistry. 1997 Mar 4;36(9):2531-8. PMID:9054558<ref>PMID:9054558</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1iow" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The crystallographic structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli complexed with a D-Ala-D-alpha-hydroxybutyrate phosphonate and the structure of the Y216F mutant ligase complexed with a D-Ala-D-Ala phosphinate have been determined to 2.2 and 1.9 A resolution, respectively, and refined to R factors of 0.156 and 0.158. In each complex the inhibitor has reacted with ATP to produce ADP and a tight-binding phosphorylated transition state intermediate. Comparison of these two structures with the known crystal structure of the phosphinate intermediate of the wild-type ligase shows no major conformational changes, but B factors indicate differences in mobility of loops covering the binding site. The weaker inhibition of the Y216F mutant by both inhibitors is thought to be due in part to the loss of an interloop hydrogen bond. A similar mechanism may account for poor inhibition of VanA, the homologous D-Ala:D-lactate ligase produced by vancomycin-resistant enterococci.
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*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1IOW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IOW OCA].
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__TOC__
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</StructureSection>
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==Reference==
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D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant., Fan C, Park IS, Walsh CT, Knox JR, Biochemistry. 1997 Mar 4;36(9):2531-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9054558 9054558]
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[[Category: D-alanine--D-alanine ligase]]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Fan, C.]]
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[[Category: Fan C]]
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[[Category: Knox, J R.]]
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[[Category: Knox JR]]
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[[Category: Moews, P C.]]
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[[Category: Moews PC]]
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[[Category: ADP]]
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[[Category: MG]]
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[[Category: PHY]]
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[[Category: adp binding]]
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[[Category: cell wall]]
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[[Category: glycogen phosphorylase]]
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[[Category: ligase]]
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[[Category: peptidoglycan synthesis]]
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[[Category: vancomycin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 12:14:37 2008''
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Current revision

COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE

PDB ID 1iow

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