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.

4q0v

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribulose

Structural highlights

4q0v 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 1.98Å
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/4q0v"

@@ Line 3: / Line 3: @@
 <StructureSection load='4q0v' size='340' side='right'caption='[[4q0v]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4q0v]] 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=4Q0V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4q0v]] 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=4Q0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q0V FirstGlance]. <br>
-</td></tr><tr id='ligand'><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></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]] 1.98&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4q0p|4q0p]], [[4q0q|4q0q]], [[4q0s|4q0s]], [[4q0u|4q0u]]</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='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=4q0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0v OCA], [https://pdbe.org/4q0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q0v RCSB], [https://www.ebi.ac.uk/pdbsum/4q0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0v 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=4q0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0v OCA], [http://pdbe.org/4q0v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q0v RCSB], [http://www.ebi.ac.uk/pdbsum/4q0v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0v 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 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Acinetobacter sp. dl-28]]
+[[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]]

4q0v

From Proteopedia

Current revision

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribulose

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox