1tal: Difference between revisions

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-{{Seed}}
-[[Image:1tal.png|left|200px]]
-<!--
+==ALPHA-LYTIC PROTEASE AT 120 K (SINGLE STRUCTURE MODEL)==
-The line below this paragraph, containing "STRUCTURE_1tal", creates the "Structure Box" on the page.
+<StructureSection load='1tal' size='340' side='right'caption='[[1tal]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1tal]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TAL FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene></td></tr>
-{{STRUCTURE_1tal|  PDB=1tal  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tal OCA], [https://pdbe.org/1tal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tal RCSB], [https://www.ebi.ac.uk/pdbsum/1tal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tal ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PRLA_LYSEN PRLA_LYSEN]
+== 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/ta/1tal_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=1tal ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Insight into the dynamic properties of alpha-lytic protease (alpha LP) has been obtained through the use of low-temperature X-ray crystallography and multiple-conformation refinement. Previous studies of alpha LP have shown that the residues around the active site are able to move significantly to accommodate substrates of different sizes. Here we show a link between the ability to accommodate ligands and the dynamics of the binding pocket. Although the structure of alpha LP at 120 K has B-factors with a uniformly low value of 4.8 A2 for the main chain, four regions stand out as having significantly higher B-factors. Because thermal motion should be suppressed at cryogenic temperatures, the high B-factors are interpreted as the result of trapped conformational substates. The active site residues that are perturbed during accommodation of different substrates are precisely those showing conformational substates, implying that substrate binding selects a subset of conformations from the ensemble of accessible states. To better characterize the precise nature of these substates, a protein model consisting of 16 structures has been refined and evaluated. The model reveals a number of features that could not be well-described by conventional B-factors: for example, 40% of the main-chain residue conformations are distributed asymmetrically or in discrete clusters. Furthermore, these data demonstrate an unexpected correlation between motions on either side of the binding pocket that we suggest is a consequence of "dynamic close packing." These results provide strong evidence for the role of protein dynamics in substrate binding and are consistent with the results of dynamic studies of ligand binding in myoglobin and ribonuclease A.
-===ALPHA-LYTIC PROTEASE AT 120 K (SINGLE STRUCTURE MODEL)===
+Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution.,Rader SD, Agard DA Protein Sci. 1997 Jul;6(7):1375-86. PMID:9232638<ref>PMID:9232638</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1tal" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9232638}}, adds the Publication Abstract to the page
+*[[Alpha-lytic protease 3D structures|Alpha-lytic protease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9232638 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9232638}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-TAL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TAL OCA].
-==Reference==
-Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution., Rader SD, Agard DA, Protein Sci. 1997 Jul;6(7):1375-86. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9232638 9232638]
-[[Category: Alpha-lytic endopeptidase]]
 [[Category: Lysobacter enzymogenes]]
-[[Category: Single protein]]
+[[Category: Agard DA]]
-[[Category: Agard, D A.]]
+[[Category: Rader SD]]
-[[Category: Rader, S D.]]
-[[Category: Hydrolase]]
-[[Category: Low temperature]]
-[[Category: Serine protease]]
-[[Category: Serine proteinase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 11:55:14 2008''