1zdp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:07, 23 August 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1zdp.png|left|200px]]
 
-
{{STRUCTURE_1zdp| PDB=1zdp | SCENE= }}
+
==Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-thiorphan==
 +
<StructureSection load='1zdp' size='340' side='right'caption='[[1zdp]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1zdp]] 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=1ZDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZDP 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]] 1.7&#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=TIO:(2-MERCAPTOMETHYL-3-PHENYL-PROPIONYL)-GLYCINE'>TIO</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=1zdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zdp OCA], [https://pdbe.org/1zdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zdp RCSB], [https://www.ebi.ac.uk/pdbsum/1zdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zdp 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/zd/1zdp_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=1zdp ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The three-dimensional structures of (S)-thiorphan and (R)-retro-thiorphan bound to thermolysin have been determined crystallographically and refined to residuals of 0.183 and 0.187 at 1.7-A resolution. Thiorphan [N-[(S)-2-(mercaptomethyl)-1-oxo-3-phenylpropyl]glycine] [HSCH2CH(CH2C6H5)CONHC-H2COOH] and retro-thiorphan [[[(R)-1-(mercaptomethyl)-2-phenylethyl] amino]-3-oxopropanoic acid] [HSCH2CH(CH2C6H5)NHCOCH2COOH] are isomeric thiol-containing inhibitors of endopeptidase EC 24-11 (also called "enkephalinase"). The mode of binding of thiorphan to thermolysin is similar to that of (2-benzyl-3-mercaptopropanoyl)-L-alanylglycinamide [Monzingo, A.F., &amp; Matthews, B.W. (1982) Biochemistry 21, 3390-3394] with the inhibitor sulfur atom coordinated to the active site zinc and the peptide portion forming substrate-like interactions with the enzyme. The isomeric inhibitor retro-thiorphan, which differs from thiorphan by the inversion of an amide bond, utilizes very similar interactions with enzyme. Despite the inversion of the -CO-NH- linkage the carbonyl oxygen and amide nitrogen display very similar hydrogen bonding, as anticipated by B.P. Roques et al. [(1983) Proc. Natl. Acad. Sci. U.S.A. 80, 3178-3182]. These results explain why thermolysin and possibly other zinc endopeptidases such as endopeptidase EC 24-11 fail to discriminate between these retro-inverso inhibitors.
-
===Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-thiorphan===
+
Thiorphan and retro-thiorphan display equivalent interactions when bound to crystalline thermolysin.,Roderick SL, Fournie-Zaluski MC, Roques BP, Matthews BW Biochemistry. 1989 Feb 21;28(4):1493-7. PMID:2719912<ref>PMID:2719912</ref>
-
{{ABSTRACT_PUBMED_2719912}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 1zdp" style="background-color:#fffaf0;"></div>
-
[[1zdp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZDP OCA].
+
==See Also==
==See Also==
-
*[[Thermolysin|Thermolysin]]
+
*[[Thermolysin 3D structures|Thermolysin 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:002719912</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
[[Category: Bacillus thermoproteolyticus]]
[[Category: Bacillus thermoproteolyticus]]
-
[[Category: Thermolysin]]
+
[[Category: Large Structures]]
-
[[Category: Fournie-Zaluski, M C.]]
+
[[Category: Fournie-Zaluski MC]]
-
[[Category: Matthews, B W.]]
+
[[Category: Matthews BW]]
-
[[Category: Roderick, S L.]]
+
[[Category: Roderick SL]]
-
[[Category: Roques, B P.]]
+
[[Category: Roques BP]]
-
[[Category: Enzyme-inhibitor complex]]
+
-
[[Category: Gamma turn]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Thermostable]]
+
-
[[Category: Zinc endopeptidase]]
+

Current revision

Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-thiorphan

PDB ID 1zdp

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools