1oud: Difference between revisions

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-[[Image:1oud.jpg|left|200px]]
- {{Structure
+==CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE STABILITY OF HUMAN LYSOZYME: X-RAY STRUCTURE OF THE V121A MUTANT==
-|PDB= 1oud |SIZE=350|CAPTION= <scene name='initialview01'>1oud</scene>, resolution 1.8&Aring;
+<StructureSection load='1oud' size='340' side='right'caption='[[1oud]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
+<table><tr><td colspan='2'>[[1oud]] is a 1 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=1OUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OUD FirstGlance]. <br>
-|ACTIVITY= [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]
+</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>
-|GENE= HUMAN LYSOZYME WITH VAL 121 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=1oud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oud OCA], [https://pdbe.org/1oud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oud RCSB], [https://www.ebi.ac.uk/pdbsum/1oud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oud 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/ou/1oud_consurf.spt"</scriptWhenChecked>
+    <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/main_output.php?pdb_ID=1oud ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+To clarify the contribution of the hydrophobic effect to the conformational stability of human lysozyme, a series of Val to Ala mutants were constructed. The thermodynamic parameters for the denaturation of these nine mutant proteins were determined using differential scanning calorimetry (DSC), and the crystal structures were solved at high resolution. The denaturation Gibbs energy (delta delta G) and enthalpy (delta delta H) values of the mutant proteins ranged from +2.2 to- 6.3 kJ/mol and from +7 to -17 kJ/mol, respectively. The structural analyses showed that the mutation site and/or the residues around it in some proteins shifted toward the created cavity, and the substitutions affected not only the mutations site but also other parts far from the site, although the structural changes were not as great. Correlation between the changes in the thermodynamic parameters and the structural features of mutant proteins was examined, including the five Ile to Val mutant human lysozymes [Takano et al. (1995) J. Mol. Biol. 254, 62-76]. There was no simple general correlation between delta delta G and the changes in hydrophobic surface area exposed upon denaturation (delta delta ASAHP). We found only a new correlation between the delta delta G and delta delta ASAHP of all of the hydrophobic residues if the effect of the secondary structure propensity was taken into account.
-'''CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE STABILITY OF HUMAN LYSOZYME: X-RAY STRUCTURE OF THE V121A MUTANT'''
+Contribution of the hydrophobic effect to the stability of human lysozyme: calorimetric studies and X-ray structural analyses of the nine valine to alanine mutants.,Takano K, Yamagata Y, Fujii S, Yutani K Biochemistry. 1997 Jan 28;36(4):688-98. PMID:9020766<ref>PMID:9020766</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1oud" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The physicochemical properties of an amyloidogenic mutant human lysozyme (Ile56Thr) were examined in order to elucidate the mechanism of amyloid formation. The crystal structure of the mutant protein was the same as the wild-type structure, except that the hydroxyl group of the introduced Thr56 formed a hydrogen bond with a water molecule in the interior of the protein. The other physicochemical properties of the mutant protein in the native state were not different from those of the wild-type protein. However, the equilibrium and kinetic stabilities of the mutant protein were remarkably decreased due to the introduction of a polar residue (Thr) in the interior of the molecule. It can be concluded that the amyloid formation of the mutant human lysozyme is due to a tendency to favor (partly or/and completely) denatured structures.
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==Disease==
+<references/>
-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]]
+__TOC__
+</StructureSection>
-==About this Structure==
-OUD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OUD OCA].
-==Reference==
-The structure, stability, and folding process of amyloidogenic mutant human lysozyme., Funahashi J, Takano K, Ogasahara K, Yamagata Y, Yutani K, J Biochem. 1996 Dec;120(6):1216-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9010773 9010773]
 [[Category: Homo sapiens]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Fujii S]]
-[[Category: Fujii, S.]]
+[[Category: Takano K]]
-[[Category: Takano, K.]]
+[[Category: Yamagata Y]]
-[[Category: Yamagata, Y.]]
+[[Category: Yutani K]]
-[[Category: Yutani, K.]]
-[[Category: NA]]
-[[Category: amyloid]]
-[[Category: disease mutation]]
-[[Category: hydrolase (o-glycosyl)]]
-[[Category: signal]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:15:42 2008''