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.


4guj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:56, 14 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==1.50 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) in Complex with Shikimate==
==1.50 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) in Complex with Shikimate==
-
<StructureSection load='4guj' size='340' side='right' caption='[[4guj]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+
<StructureSection load='4guj' size='340' side='right'caption='[[4guj]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4guj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GUJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GUJ FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4guj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GUJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GUJ FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4guf|4guf]], [[4gug|4gug]], [[4guh|4guh]], [[4gui|4gui]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aroD, STM1358 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=4guj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4guj OCA], [https://pdbe.org/4guj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4guj RCSB], [https://www.ebi.ac.uk/pdbsum/4guj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4guj ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-dehydroquinate_dehydratase 3-dehydroquinate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.10 4.2.1.10] </span></td></tr>
+
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4guj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4guj OCA], [http://pdbe.org/4guj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4guj RCSB], [http://www.ebi.ac.uk/pdbsum/4guj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4guj ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/AROD_SALTY AROD_SALTY]
-
A component of the shikimate biosynthetic pathway, dehydroquinate dehydratase (DHQD) catalyzes the dehydration of 3-dehydroquniate (DHQ) to 3-dehydroshikimate. In the type I DHQD reaction mechanism a lysine forms a Schiff base intermediate with DHQ. The Schiff base acts as an electron sink to facilitate the catalytic dehydration. To address the mechanism of Schiff base formation, we determined structures of the Salmonella enterica wild-type DHQD in complex with the substrate analogue quinate and the product analogue shikimate. In addition, we determined the structure of the K170M mutant (Lys170 being the Schiff base forming residue) in complex with quinate. Combined with nuclear magnetic resonance and isothermal titration calorimetry data that revealed altered binding of the analogue to the K170M mutant, these structures suggest a model of Schiff base formation characterized by the dynamic interplay of opposing forces acting on either side of the substrate. On the side distant from the substrate 3-carbonyl group, closure of the enzyme's beta8-alpha8 loop is proposed to guide DHQ into the proximity of the Schiff base-forming Lys170. On the 3-carbonyl side of the substrate, Lys170 sterically alters the position of DHQ's reactive ketone, aligning it at an angle conducive for nucleophilic attack. This study of a type I DHQD reveals the interplay between the enzyme and substrate required for the correct orientation of a functional group constrained within a cyclic substrate.
+
-
Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of Schiff base formation.,Light SH, Antanasijevic A, Krishna SN, Caffrey M, Anderson WF, Lavie A Biochemistry. 2014 Feb 11;53(5):872-80. doi: 10.1021/bi4015506. Epub 2014 Jan 31. PMID:24437575<ref>PMID:24437575</ref>
+
==See Also==
-
 
+
*[[Dehydroquinase 3D structures|Dehydroquinase 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4guj" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: 3-dehydroquinate dehydratase]]
+
[[Category: Large Structures]]
-
[[Category: Salty]]
+
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-
[[Category: Anderson, W F]]
+
[[Category: Anderson WF]]
-
[[Category: Structural genomic]]
+
[[Category: Duban M-E]]
-
[[Category: Duban, M E]]
+
[[Category: Kwon K]]
-
[[Category: Kwon, K]]
+
[[Category: Lavie A]]
-
[[Category: Lavie, A]]
+
[[Category: Light SH]]
-
[[Category: Light, S H]]
+
[[Category: Minasov G]]
-
[[Category: Minasov, G]]
+
[[Category: Shuvalova L]]
-
[[Category: Shuvalova, L]]
+
-
[[Category: Csgid]]
+
-
[[Category: Lyase]]
+
-
[[Category: National institute of allergy and infectious disease]]
+
-
[[Category: Niaid]]
+
-
[[Category: Tim barrel]]
+

Current revision

1.50 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) in Complex with Shikimate

PDB ID 4guj

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/4guj"
Personal tools