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.


4z1a

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:04, 20 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Structure of apo form KDO8PS from H.pylori==
==Structure of apo form KDO8PS from H.pylori==
-
<StructureSection load='4z1a' size='340' side='right' caption='[[4z1a]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+
<StructureSection load='4z1a' size='340' side='right'caption='[[4z1a]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4z1a]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z1A FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4z1a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z1A FirstGlance]. <br>
-
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4z1b|4z1b]], [[4z1c|4z1c]], [[4z1d|4z1d]]</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]] 2&#8491;</td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </span></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=4z1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z1a OCA], [https://pdbe.org/4z1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z1a RCSB], [https://www.ebi.ac.uk/pdbsum/4z1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z1a ProSAT]</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=4z1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z1a OCA], [http://pdbe.org/4z1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z1a RCSB], [http://www.ebi.ac.uk/pdbsum/4z1a PDBsum]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/KDSA_HELPY KDSA_HELPY]
-
The crystal structure of 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDO8PS) from Helicobacter pylori (HpKDO8PS) was determined alone and within various complexes, revealing an extra helix (HE) that is absent in the structures of KDO8PS from other organisms. In contrast to the metal coordination of the KDO8PS enzyme from Aquifex aeolicus, HpKDO8PS is specifically coordinated with Cd(2+) or Zn(2+) ions, and isothermal titration calorimetry (ITC) and differential scanning fluorimetry (DSF) revealed that Cd(2+) thermally stabilizes the protein structure more efficiently than Zn(2+). In the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure. Using the structures of HpKDO8PS and API [arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) bisubstrate inhibitor], we generated 21 compounds showing potential HpKDO8PS-binding properties via in silico virtual screening. The capacity of three, avicularin, hyperin, and MC181, to bind to HpKDO8PS was confirmed through saturation transfer difference (STD) experiments, and we identified their specific ligand binding modes by combining competition experiments and docking simulation analysis. Hyperin was confirmed to bind to the A5P binding site, primarily via hydrophilic interaction, whereas MC181 bound to both the PEP and A5P binding sites through hydrophilic and hydrophobic interactions. These results were consistent with the epitope mapping by STD. Our results are expected to provide clues for the development of HpKDO8PS inhibitors.
+
-
Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS).,Cho S, Im H, Lee KY, Chen J, Kang HJ, Yoon HJ, Min KH, Lee KR, Park HJ, Lee BJ Eur J Med Chem. 2016 Jan 27;108:188-202. doi: 10.1016/j.ejmech.2015.11.036. Epub , 2015 Dec 1. PMID:26649906<ref>PMID:26649906</ref>
+
==See Also==
-
 
+
*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4z1a" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: 3-deoxy-8-phosphooctulonate synthase]]
+
[[Category: Helicobacter pylori 26695]]
-
[[Category: Cho, S]]
+
[[Category: Large Structures]]
-
[[Category: Im, H]]
+
[[Category: Cho S]]
-
[[Category: Lee, B J]]
+
[[Category: Im H]]
-
[[Category: Yoon, H J]]
+
[[Category: Lee BJ]]
-
[[Category: Apo]]
+
[[Category: Yoon HJ]]
-
[[Category: Helicobacter pylori]]
+
-
[[Category: Lipopolysaccharide biosynthesis]]
+
-
[[Category: Transferase]]
+

Current revision

Structure of apo form KDO8PS from H.pylori

PDB ID 4z1a

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/4z1a"
Personal tools