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.


4q0q

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:03, 8 November 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with L-ribulose==
==Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with L-ribulose==
-
<StructureSection load='4q0q' size='340' side='right' caption='[[4q0q]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
+
<StructureSection load='4q0q' size='340' side='right'caption='[[4q0q]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4q0q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0Q FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4q0q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_sp._DL-28 Acinetobacter sp. DL-28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q0Q FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=QDK:L-RIBULOSE'>QDK</scene>, <scene name='pdbligand=RUU:ALPHA-L-RIBULOFURANOSE'>RUU</scene><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]] 1.93&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4q0p|4q0p]], [[4q0s|4q0s]], [[4q0u|4q0u]], [[4q0v|4q0v]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=QDK:L-RIBULOSE'>QDK</scene>, <scene name='pdbligand=RUU:ALPHA-L-RIBULOFURANOSE'>RUU</scene></td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4q0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q0q RCSB], [http://www.ebi.ac.uk/pdbsum/4q0q PDBsum]</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=4q0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0q OCA], [https://pdbe.org/4q0q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q0q RCSB], [https://www.ebi.ac.uk/pdbsum/4q0q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0q ProSAT]</span></td></tr>
-
<table>
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q93UQ5_9GAMM Q93UQ5_9GAMM]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
-
Acinetobacter sp. L-ribose isomerase (L-RI) catalyzes a reversible isomerization reaction between L-ribose and L-ribulose. To date, information on L-RI remains limited and its amino-acid sequence shows no similarity to those of any known enzymes. Here, recombinant His-tagged L-RI was successfully overexpressed, purified and crystallized. Crystals of His-tagged L-RI were obtained by the hanging-drop vapour-diffusion method at room temperature as two crystal forms which belonged to the monoclinic space group C2, with unit-cell parameters a = 96.60, b = 105.89, c = 71.83 A, beta = 118.16 degrees , and the orthorhombic space group F222, with unit-cell parameters a = 96.44, b = 106.26, c = 117.83 A. Diffraction data were collected to 3.1 and 2.2 A resolution, respectively.
+
l-Ribose, a pentose, is not known to exist in nature. Although organisms typically do not have a metabolic pathway that uses l-ribose as a carbon source, prokaryotes use various sugars as carbon sources for survival. Acinetobacter sp. DL-28 has been shown to express the novel enzyme, l-ribose isomerase (AcL-RbI), which catalyzes reversible isomerization between l-ribose and l-ribulose. AcL-RbI showed the highest activity to l-ribose, followed by d-lyxose with 47% activity, and had no significant amino acid sequence similarity to structure-known proteins, except for weak homology with the d-lyxose isomerases from Escherichia coli O157 : H7 (18%) and Bacillus subtilis strain (19%). Thus, AcL-RbI is expected to have the unique three-dimensional structure to recognize l-ribose as its ideal substrate. The X-ray structures of AcL-RbI in complexes with substrates were determined. AcL-RbI had a cupin-type beta-barrel structure, and the catalytic site was found between two large beta-sheets with a bound metal ion. The catalytic site structures clearly showed that AcL-RbI adopted a cis-enediol intermediate mechanism for the isomerization reaction using two glutamate residues (Glu113 and Glu204) as acid/base catalysts. In its crystal form, AcL-RbI formed a unique homotetramer with many substrate sub-binding sites, which likely facilitated capture of the substrate. DATABASE: The atomic coordinates and structure factors of AcL-RbI/l-ribose, AcL-RbI/l-ribulose, AcL-RbI/ribitol, E204Q/l-ribose and E204Q/l-ribulose have been deposited in the Protein Data Bank under accession codes, 4Q0P, 4Q0Q, 4Q0S, 4Q0U and 4Q0V. STRUCTURED DIGITAL ABSTRACT: * AcL-RbI and AcL-RbI bind by x-ray crystallography (View interaction).
-
Overexpression, crystallization and preliminary X-ray diffraction analysis of L-ribose isomerase from Acinetobacter sp. strain DL-28.,Yoshida H, Teraoka M, Yoshihara A, Izumori K, Kamitori S Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Oct 1;67(Pt 10):1281-4., doi: 10.1107/S1744309111030351. Epub 2011 Sep 30. PMID:22102048<ref>PMID:22102048</ref>
+
X-ray structure of a novel l-ribose isomerase acting on a non-natural sugar l-ribose as its ideal substrate.,Yoshida H, Yoshihara A, Teraoka M, Terami Y, Takata G, Izumori K, Kamitori S FEBS J. 2014 May 20. doi: 10.1111/febs.12850. PMID:24846739<ref>PMID:24846739</ref>
-
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
 +
<div class="pdbe-citations 4q0q" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Izumori, K.]]
+
[[Category: Acinetobacter sp. DL-28]]
-
[[Category: Kamitori, S.]]
+
[[Category: Large Structures]]
-
[[Category: Teraoka, M.]]
+
[[Category: Izumori K]]
-
[[Category: Yoshida, H.]]
+
[[Category: Kamitori S]]
-
[[Category: Yoshihara, A.]]
+
[[Category: Teraoka M]]
-
[[Category: Cupin barrel]]
+
[[Category: Yoshida H]]
-
[[Category: Isomerase]]
+
[[Category: Yoshihara A]]
-
[[Category: Sugar binding]]
+

Current revision

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with L-ribulose

PDB ID 4q0q

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/4q0q"
Personal tools