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1nhb

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[[Image:1nhb.gif|left|200px]]<br /><applet load="1nhb" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1nhb, resolution 1.80&Aring;" />
 
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'''SPECIFICITY OF LIGAND BINDING IN A BURIED NON-POLAR CAVITY OF T4 LYSOZYME: LINKAGE OF DYNAMICS AND STRUCTURAL PLASTICITY'''<br />
 
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==Overview==
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==Specificity of ligand binding in a buried non-polar cavity of t4 lysozyme: linkage of dynamics and structural plasticity==
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To better understand the role of shape complementarity in ligand binding and protein core interactions, the structures have been determined of a set of ligands bound within a cavity-containing mutant of T4 lysozyme. The interior cavity is seen to consist of two parts that respond very differently to the binding of ligands. First, there is a relatively rigid region that does not relax significantly upon binding any ligand. Second, there is a more flexible region that moves to various extents in response to binding the different ligands. The part of the binding site that remains rigid is characterized by low temperature factors and strong protection from hydrogen exchange. This part of the site appears to be primarily responsible for discriminating between ligands of different shape (i.e., for determining specificity). The more flexible region, characterized by relatively high temperature factors and weak protection from hydrogen exchange, allows some promiscuity in binding by undergoing variable amounts of deformation at essentially the same energetic cost. This linkage between the dynamic information represented by crystallographic temperature factors and hydrogen-exchange behavior on the one hand, and structural plasticity in response to ligand binding on the other hand, suggests a way to improve our understanding of steric interactions in protein cores and protein-ligand binding sites. Ligand design and packing algorithms might take advantage of this information, requiring complementary interactions where the protein is rigid and allowing some overlap in regions where the protein is flexible.
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<StructureSection load='1nhb' size='340' side='right'caption='[[1nhb]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1nhb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NHB FirstGlance]. <br>
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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]] 1.8&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=PYJ:PHENYLETHANE'>PYJ</scene></td></tr>
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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=1nhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhb OCA], [https://pdbe.org/1nhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nhb RCSB], [https://www.ebi.ac.uk/pdbsum/1nhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nhb ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
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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/nh/1nhb_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=1nhb ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1NHB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=HED:'>HED</scene> and <scene name='pdbligand=PYL:'>PYL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHB OCA].
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
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== References ==
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==Reference==
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<references/>
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Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity., Morton A, Matthews BW, Biochemistry. 1995 Jul 11;34(27):8576-88. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7612599 7612599]
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__TOC__
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[[Category: Bacteriophage t4]]
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</StructureSection>
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[[Category: Lysozyme]]
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[[Category: Escherichia virus T4]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Matthews, B W.]]
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[[Category: Matthews BW]]
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[[Category: Morton, A.]]
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[[Category: Morton A]]
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[[Category: CL]]
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[[Category: HED]]
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[[Category: PYL]]
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[[Category: hydrolase (o-glycosyl)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:06:03 2008''
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Current revision

Specificity of ligand binding in a buried non-polar cavity of t4 lysozyme: linkage of dynamics and structural plasticity

PDB ID 1nhb

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