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.


4q0p

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:51, 3 April 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 3: Line 3:
<StructureSection load='4q0p' size='340' side='right'caption='[[4q0p]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
<StructureSection load='4q0p' size='340' side='right'caption='[[4q0p]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4q0p]] is a 1 chain structure with sequence from [http://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=4Q0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0P FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4q0p]] 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=4Q0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q0P FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0MK:L-RIBOPYRANOSE'>0MK</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=Z6J:ALPHA-L-RIBOFURANOSE'>Z6J</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]] 1.93&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4q0q|4q0q]], [[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=0MK:L-RIBOPYRANOSE'>0MK</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=Z6J:ALPHA-L-RIBOFURANOSE'>Z6J</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">L-RI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160971 Acinetobacter sp. DL-28])</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=4q0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0p OCA], [https://pdbe.org/4q0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q0p RCSB], [https://www.ebi.ac.uk/pdbsum/4q0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0p 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=4q0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0p OCA], [http://pdbe.org/4q0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q0p RCSB], [http://www.ebi.ac.uk/pdbsum/4q0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0p ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q93UQ5_9GAMM Q93UQ5_9GAMM]
-
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).
+
-
 
+
-
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4q0p" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Acinetobacter sp. dl-28]]
+
[[Category: Acinetobacter sp. DL-28]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Izumori, K]]
+
[[Category: Izumori K]]
-
[[Category: Kamitori, S]]
+
[[Category: Kamitori S]]
-
[[Category: Teraoka, M]]
+
[[Category: Teraoka M]]
-
[[Category: Yoshida, H]]
+
[[Category: Yoshida H]]
-
[[Category: Yoshihara, A]]
+
[[Category: Yoshihara A]]
-
[[Category: Cupin barrel]]
+
-
[[Category: Isomerase]]
+
-
[[Category: Sugar binding]]
+

Current revision

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

PDB ID 4q0p

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/4q0p"
Personal tools