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.


2xhz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:32, 20 December 2023) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2xhz.jpg|left|200px]]
 
-
<!--
+
==Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography==
-
The line below this paragraph, containing "STRUCTURE_2xhz", creates the "Structure Box" on the page.
+
<StructureSection load='2xhz' size='340' side='right'caption='[[2xhz]], [[Resolution|resolution]] 2.60&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'>[[2xhz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XHZ 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]] 2.6&#8491;</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=2xhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhz OCA], [https://pdbe.org/2xhz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xhz RCSB], [https://www.ebi.ac.uk/pdbsum/2xhz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhz ProSAT]</span></td></tr>
-
{{STRUCTURE_2xhz| PDB=2xhz | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/KDSD_ECOLI KDSD_ECOLI] Involved in the biosynthesis of 3-deoxy-D-manno-octulosonate (KDO), a unique 8-carbon sugar component of lipopolysaccharides (LPSs). KdsD is not essential in the KDO biosynthesis and can be substituted by GutQ. Catalyzes the reversible aldol-ketol isomerization between D-ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P).<ref>PMID:12805358</ref> <ref>PMID:16199563</ref> <ref>PMID:16765569</ref>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Lipopolysaccharide (LPS) biosynthesis represents an underexploited target pathway for novel antimicrobial development to combat the emergence of multidrug-resistant bacteria. A key player in LPS synthesis is the enzyme D-arabinose-5-phosphate isomerase (API), which catalyzes the reversible isomerization of D-ribulose-5-phosphate to D-arabinose-5-phosphate, a precursor of 3-deoxy-D-manno-octulosonate that is an essential residue of the LPS inner core. API is composed of two main domains: an N-terminal sugar isomerase domain (SIS) and a pair of cystathionine-beta-synthase domains of unknown function. As the three-dimensional structure of an enzyme is a prerequisite for the rational development of novel inhibitors, we present here the crystal structure of the SIS domain of a catalytic mutant (K59A) of E. coli D-arabinose-5-phosphate isomerase at 2.6-A resolution. Our structural analyses and comparisons made with other SIS domains highlight several potentially important active site residues. In particular, the crystal structure allowed us to identify a previously unpredicted His residue (H88) located at the mouth of the active site cavity as a possible catalytic residue. On the basis of such structural data, subsequently supported by biochemical and mutational experiments, we confirm the catalytic role of H88, which appears to be a generally conserved residue among two-domain isomerases.
-
===PROBING THE ACTIVE SITE OF THE SUGAR ISOMERASE DOMAIN FROM E. COLI ARABINOSE-5-PHOSPHATE ISOMERASE VIA X-RAY CRYSTALLOGRAPHY===
+
Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography.,Gourlay LJ, Sommaruga S, Nardini M, Sperandeo P, Deho G, Polissi A, Bolognesi M Protein Sci. 2010 Dec;19(12):2430-9. doi: 10.1002/pro.525. PMID:20954237<ref>PMID:20954237</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_20954237}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2xhz" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 20954237 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20954237}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
[[2xhz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHZ OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:20954237</ref><references group="xtra"/>
+
-
[[Category: Arabinose-5-phosphate isomerase]]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Bolognesi, M.]]
+
[[Category: Large Structures]]
-
[[Category: Deho, G.]]
+
[[Category: Bolognesi M]]
-
[[Category: Gourlay, L J.]]
+
[[Category: Deho G]]
-
[[Category: Nardini, M.]]
+
[[Category: Gourlay LJ]]
-
[[Category: Polissi, A.]]
+
[[Category: Nardini M]]
-
[[Category: Sommaruga, S.]]
+
[[Category: Polissi A]]
-
[[Category: Sperandeo, P.]]
+
[[Category: Sommaruga S]]
 +
[[Category: Sperandeo P]]

Current revision

Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography

PDB ID 2xhz

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/2xhz"
Personal tools