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.

3sgw

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 18:36, 1 February 2017

Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid

Structural highlights

3sgw is a 1 chain structure with sequence from Cocim. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	3qd5, 3sdw, 3s5p
Gene:	CIMG_07932 (COCIM)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

ABSTRACT: BACKGROUND: Ribose-5-phosphate isomerase is an enzyme that catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate. This family of enzymes naturally occurs in two distinct classes, RpiA and RpiB, which play an important role in the pentose phosphate pathway and nucleotide and co-factor biogenesis. RESULTS: Although RpiB occurs predominantly in bacteria, here we report crystal structures of a putative RpiB from the pathogenic fungus Coccidioides immitis. A 1.9 A resolution apo structure was solved by combined molecular replacement and single wavelength anomalous dispersion (SAD) phasing using a crystal soaked briefly in a solution containing a high concentration of iodide ions. RpiB from C. immitis contains modest sequence and high structural homology to other known RpiB structures. A 1.8 A resolution phosphate-bound structure demonstrates phosphate recognition and charge stabilization by a single positively charged residue whereas other members of this family use up to five positively charged residues to contact the phosphate of ribose-5-phosphate. A 1.7 A resolution structure was obtained in which the catalytic base of C. immitis RpiB, Cys76, appears to form a weakly covalent bond with the central carbon of malonic acid with a bond distance of 2.2 A. This interaction may mimic that formed by the suicide inhibitor iodoacetic acid with RpiB. CONCLUSION: The C. immitis RpiB contains the same fold and similar features as other members of this class of enzymes such as a highly reactive active site cysteine residue, but utilizes a divergent phosphate recognition strategy and may recognize a different substrate altogether.

Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis.,Edwards TE, Abramov AB, Smith ER, Baydo RO, Leonard JT, Leibly DJ, Thompkins KB, Clifton MC, Gardberg AS, Staker BL, Van Voorhis WC, Myler PJ, Stewart LJ BMC Struct Biol. 2011 Oct 13;11(1):39. PMID:21995815^[1]

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

References

↑ Edwards TE, Abramov AB, Smith ER, Baydo RO, Leonard JT, Leibly DJ, Thompkins KB, Clifton MC, Gardberg AS, Staker BL, Van Voorhis WC, Myler PJ, Stewart LJ. Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis. BMC Struct Biol. 2011 Oct 13;11(1):39. PMID:21995815 doi:10.1186/1472-6807-11-39

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3sgw"

@@ Line 1: / Line 1: @@
 ==Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid==
 <StructureSection load='3sgw' size='340' side='right' caption='[[3sgw]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qd5|3qd5]], [[3sdw|3sdw]], [[3s5p|3s5p]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CIMG_07932 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246410 COCIM])</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=3sgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sgw RCSB], [http://www.ebi.ac.uk/pdbsum/3sgw PDBsum]</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=3sgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgw OCA], [http://pdbe.org/3sgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sgw RCSB], [http://www.ebi.ac.uk/pdbsum/3sgw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sgw ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 16: / Line 17: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3sgw" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Ribose-5-phosphate isomerase|Ribose-5-phosphate isomerase]]
 == References ==
 <references/>

3sgw

From Proteopedia

Revision as of 18:36, 1 February 2017

Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox