1lnb: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1lnb.jpg|left|200px]]
-<!--
+==A STRUCTURAL ANALYSIS OF METAL SUBSTITUTIONS IN THERMOLYSIN==
-The line below this paragraph, containing "STRUCTURE_1lnb", creates the "Structure Box" on the page.
+<StructureSection load='1lnb' size='340' side='right'caption='[[1lnb]], [[Resolution|resolution]] 1.80&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'>[[1lnb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LNB 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene></td></tr>
-{{STRUCTURE_1lnb|  PDB=1lnb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lnb OCA], [https://pdbe.org/1lnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lnb RCSB], [https://www.ebi.ac.uk/pdbsum/1lnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lnb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease.
+== 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/ln/1lnb_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=1lnb ConSurf].
+<div style="clear:both"></div>
-'''A STRUCTURAL ANALYSIS OF METAL SUBSTITUTIONS IN THERMOLYSIN'''
+==See Also==
+*[[Thermolysin 3D structures|Thermolysin 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Native thermolysin binds a single catalytically essential zinc ion that is tetrahedrally coordinated by three protein ligands and a water molecule. During catalysis the zinc ligation is thought to change from fourfold to fivefold. Substitution of the active-site zinc with Cd2+, Mn2+, Fe2+, and Co2+ alters the catalytic activity (Holmquist B, Vallee BL, 1974, J Biol Chem 249:4601-4607). Excess zinc inhibits the enzyme. To investigate the structural basis of these changes in activity, we have determined the structures of a series of metal-substituted thermolysins at 1.7-1.9 A resolution. The structure of the Co(2+)-substituted enzyme is shown to be very similar to that of wild type except that two solvent molecules are liganded to the metal at positions that are thought to be occupied by the two oxygens of the hydrated scissile peptide in the transition state. Thus, the enhanced activity toward some substrates of the cobalt-relative to the zinc-substituted enzyme may be due to enhanced stabilization of the transition state. The ability of Zn2+ and Co2+ to accept tetrahedral coordination in the Michaelis complex, as well as fivefold coordination in the transition state, may also contribute to their effectiveness in catalysis. The Cd(2+)- and Mn(2+)-substituted thermolysins display conformational changes that disrupt the active site to varying degrees and could explain the associated reduction of activity. The conformational changes involve not only the essential catalytic residue, Glu 143, but also concerted side-chain rotations in the adjacent residues Met 120 and Leu 144. Some of these side-chain movements are similar to adjustments that have been observed previously in association with the "hinge-bending" motion that is presumed to occur during catalysis by the zinc endoproteases. In the presence of excess zinc, a second zinc ion is observed to bind at His 231 within 3.2 A of the zinc bound to native thermolysin, explaining the inhibitory effect.
+[[Category: Bacillus thermoproteolyticus]]
+[[Category: Large Structures]]
-==About this Structure==
+[[Category: Hausrath AC]]
-LNB is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LNB OCA].
+[[Category: Holland DR]]
+[[Category: Juers D]]
-==Reference==
+[[Category: Matthews BW]]
-Structural analysis of zinc substitutions in the active site of thermolysin., Holland DR, Hausrath AC, Juers D, Matthews BW, Protein Sci. 1995 Oct;4(10):1955-65. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8535232 8535232]
-[[Category: Single protein]]
-[[Category: Thermolysin]]
-[[Category: Hausrath, A C.]]
-[[Category: Holland, D R.]]
-[[Category: Juers, D.]]
-[[Category: Matthews, B W.]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 30 13:54:15 2008''