This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1lnf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:34, 14 February 2024) (edit) (undo)
 
(19 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1lnf.jpg|left|200px]]
 
-
{{Structure
+
==A structural analysis of metal substitutions in thermolysin==
-
|PDB= 1lnf |SIZE=350|CAPTION= <scene name='initialview01'>1lnf</scene>, resolution 1.70&Aring;
+
<StructureSection load='1lnf' size='340' side='right'caption='[[1lnf]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=DMS:DIMETHYL SULFOXIDE'>DMS</scene>
+
<table><tr><td colspan='2'>[[1lnf]] 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=1LNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LNF FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-
|GENE=
+
<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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1lnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lnf OCA], [https://pdbe.org/1lnf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lnf RCSB], [https://www.ebi.ac.uk/pdbsum/1lnf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lnf 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/1lnf_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=1lnf 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: Holland DR]]
-
1LNF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LNF OCA].
+
[[Category: Matthews BW]]
-
 
+
-
==Reference==
+
-
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: Holland, D R.]]
+
-
[[Category: Matthews, B W.]]
+
-
[[Category: CA]]
+
-
[[Category: DMS]]
+
-
[[Category: ZN]]
+
-
[[Category: hydrolase (metalloprotease)]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:32:55 2008''
+

Current revision

A structural analysis of metal substitutions in thermolysin

PDB ID 1lnf

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1lnf"
Personal tools