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1z16

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(New page: 200px<br /><applet load="1z16" size="450" color="white" frame="true" align="right" spinBox="true" caption="1z16, resolution 1.72&Aring;" /> '''Crystal structure an...)
Current revision (06:21, 3 April 2024) (edit) (undo)
 
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[[Image:1z16.gif|left|200px]]<br /><applet load="1z16" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1z16, resolution 1.72&Aring;" />
 
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'''Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound leucine'''<br />
 
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==Overview==
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==Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound leucine==
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The leucine/isoleucine/valine-binding protein (LIVBP or LivJ) serves as, the primary high-affinity receptor of the Escherichia coli ABC-type, transporter for the three aliphatic amino acids. The first structure of, LIVBP determined previously without bound ligand showed a molecule, comprised of two domains which are far apart and bisected by a wide open, solvent-accessible cleft. Here we report the crystal structures of another, ligand-free state and three complexes with the aliphatic amino acids. In, the present ligand-free structure, the two domains are farther apart. In, the three very similar complex structures, the two domains are in close, proximity, and each desolvated ligand is completely engulfed in the cleft, and bound by both domains. The two different ligand-free structures, combined with those of the very similar ligand-bound structures, indicate, the trajectory and backbone torsion angle changes of the hinges that, accompany domain closure and play crucial functional roles. The amino, acids are bound by polar and nonpolar interactions, occurring, predominantly in one domain. Consistent with the protein specificity, the, aliphatic side chains of the ligands lie in a hydrophobic pocket fully, formed following domain or cleft closure. Comparison of the structures of, LIVBP with several different binding proteins indicates no correlations, between the magnitudes of the hinge-bending angles and the protein masses, the ligand sizes, or the number of segments connecting the two domains., Results of normal-mode analysis and molecular dynamics simulations are, consistent with the trajectory and intrinsic flexibility of the, interdomain hinges and the dominance of one domain in ligand binding in, the open state.
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<StructureSection load='1z16' size='340' side='right'caption='[[1z16]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1z16]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z16 FirstGlance]. <br>
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1Z16 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with CD and LEU as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Z16 OCA].
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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]] 1.72&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene></td></tr>
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==Reference==
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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=1z16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z16 OCA], [https://pdbe.org/1z16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z16 RCSB], [https://www.ebi.ac.uk/pdbsum/1z16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z16 ProSAT]</span></td></tr>
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Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity., Trakhanov S, Vyas NK, Luecke H, Kristensen DM, Ma J, Quiocho FA, Biochemistry. 2005 May 3;44(17):6597-608. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15850393 15850393]
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</table>
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[[Category: Escherichia coli]]
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== Function ==
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[[Category: Single protein]]
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[https://www.uniprot.org/uniprot/LIVJ_ECOLI LIVJ_ECOLI] This protein is a component of the leucine, isoleucine, valine, (threonine) transport system, which is one of the two periplasmic binding protein-dependent transport systems of the high-affinity transport of the branched-chain amino acids.
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[[Category: Kristensen, D.M.]]
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== Evolutionary Conservation ==
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[[Category: Ma, J.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Quiocho, F.A.]]
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Check<jmol>
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[[Category: Trakhanov, S.D.]]
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<jmolCheckbox>
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[[Category: Vyas, N.K.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z1/1z16_consurf.spt"</scriptWhenChecked>
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[[Category: CD]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: LEU]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: aliphatic amino acid binding protein]]
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</jmolCheckbox>
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[[Category: alpha-beta fold]]
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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=1z16 ConSurf].
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[[Category: periplasmic binding proteins]]
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<div style="clear:both"></div>
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__TOC__
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:11:01 2007''
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</StructureSection>
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[[Category: Escherichia coli K-12]]
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[[Category: Large Structures]]
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[[Category: Kristensen DM]]
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[[Category: Ma J]]
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[[Category: Quiocho FA]]
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[[Category: Trakhanov SD]]
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[[Category: Vyas NK]]

Current revision

Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound leucine

PDB ID 1z16

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