1ckg: Difference between revisions

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-[[Image:1ckg.jpg|left|200px]]<br /><applet load="1ckg" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1ckg, resolution 2.2&Aring;" />
-'''T52V MUTANT HUMAN LYSOZYME'''<br />
-==Overview==
+==T52V MUTANT HUMAN LYSOZYME==
-In globular proteins, there are intermolecular hydrogen bonds between, protein and water molecules, and between water molecules, which are bound, with the proteins, in addition to intramolecular hydrogen bonds. To, estimate the contribution of these hydrogen bonds to the conformational, stability of a protein, the thermodynamic parameters for denaturation and, the crystal structures of five Thr to Val and five Thr to Ala mutant human, lysozymes were determined. The denaturation Gibbs energy (DeltaG) of Thr, to Val and Thr to Ala mutant proteins was changed from 4.0 to -5.6 kJ/mol, and from 1.6 to -6.3 kJ/mol, respectively, compared with that of the, wild-type protein. The contribution of hydrogen bonds to the stability, (DeltaDeltaG(HB)) of the Thr and other mutant human lysozymes previously, reported was extracted from the observed stability changes (DeltaDeltaG), with correction for changes in hydrophobicity and side chain, conformational entropy between the wild-type and mutant structures. The, estimation of the DeltaDeltaG(HB) values of all mutant proteins after, removal of hydrogen bonds, including protein-water hydrogen bonds, indicates a favorable contribution of the intra- and intermolecular, hydrogen bonds to the protein stability. The net contribution of an, intramolecular hydrogen bond (DeltaG(HB[pp])), an intermolecular one, between protein and ordered water molecules (DeltaG(HB[pw])), and an, intermolecular one between ordered water molecules (DeltaG(HB[ww])) could, be estimated to be 8. 5, 5.2, and 5.0 kJ/mol, respectively, for a 3 A long, hydrogen bond. This result shows the different contributions to protein, stability of intra- and intermolecular hydrogen bonds. The entropic cost, due to the introduction of a water molecule (DeltaG(H)()2(O)) could be, also estimated to be about 8 kJ/mol.
+<StructureSection load='1ckg' size='340' side='right'caption='[[1ckg]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ckg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CKG FirstGlance]. <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]] 2.2&#8491;</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=1ckg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ckg OCA], [https://pdbe.org/1ckg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ckg RCSB], [https://www.ebi.ac.uk/pdbsum/1ckg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ckg ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/LYSC_HUMAN LYSC_HUMAN] Defects in LYZ are a cause of amyloidosis type 8 (AMYL8) [MIM:[https://omim.org/entry/105200 105200]; also known as systemic non-neuropathic amyloidosis or Ostertag-type amyloidosis. AMYL8 is a hereditary generalized amyloidosis due to deposition of apolipoprotein A1, fibrinogen and lysozyme amyloids. Viscera are particularly affected. There is no involvement of the nervous system. Clinical features include renal amyloidosis resulting in nephrotic syndrome, arterial hypertension, hepatosplenomegaly, cholestasis, petechial skin rash.<ref>PMID:8464497</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/LYSC_HUMAN LYSC_HUMAN] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents.
+== 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/ck/1ckg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/main_output.php?pdb_ID=1ckg ConSurf].
+<div style="clear:both"></div>
-==Disease==
+==See Also==
-Known diseases associated with this structure: Amyloidosis, renal OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=153450 153450]], Microphthalmia, syndromic 1 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=309800 309800]]
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-CKG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. 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=1CKG OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme(,)., Takano K, Yamagata Y, Funahashi J, Hioki Y, Kuramitsu S, Yutani K, Biochemistry. 1999 Sep 28;38(39):12698-708. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10504240 10504240]
 [[Category: Homo sapiens]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Funahashi J]]
-[[Category: Funahashi, J.]]
+[[Category: Takano K]]
-[[Category: Takano, K.]]
+[[Category: Yamagata Y]]
-[[Category: Yamagata, Y.]]
+[[Category: Yutani K]]
-[[Category: Yutani, K.]]
-[[Category: hydrogen bond]]
-[[Category: stability]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 15:36:08 2008''