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4q0q

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

Structural highlights

4q0q is a 1 chain structure with sequence from Acinetobacter sp. DL-28. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.93Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q93UQ5_9GAMM

Publication Abstract from PubMed

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yoshida H, Yoshihara A, Teraoka M, Terami Y, Takata G, Izumori K, Kamitori S. X-ray structure of a novel l-ribose isomerase acting on a non-natural sugar l-ribose as its ideal substrate. FEBS J. 2014 May 20. doi: 10.1111/febs.12850. PMID:24846739 doi:http://dx.doi.org/10.1111/febs.12850

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4q0q"

@@ Line 3: / Line 3: @@
 <StructureSection load='4q0q' size='340' side='right'caption='[[4q0q]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
 == 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 [https://proteopedia.org/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 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>
+</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"><div style='overflow: auto; max-height: 3em;'>[[4q0p|4q0p]], [[4q0s|4q0s]], [[4q0u|4q0u]], [[4q0v|4q0v]]</div></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 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>
+== Function ==
+[https://www.uniprot.org/uniprot/Q93UQ5_9GAMM Q93UQ5_9GAMM]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Acinetobacter sp. DL-28]]
 [[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]]

4q0q

From Proteopedia

Current revision

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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