|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Crystal structure of a putative ribose-5-phosphate isomerase from Coccidioides immitis solved by combined iodide ion SAD and MR== | | ==Crystal structure of a putative ribose-5-phosphate isomerase from Coccidioides immitis solved by combined iodide ion SAD and MR== |
| - | <StructureSection load='3qd5' size='340' side='right' caption='[[3qd5]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='3qd5' size='340' side='right'caption='[[3qd5]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3qd5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Coccidioides_immitis Coccidioides immitis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QD5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3qd5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Coccidioides_immitis_RS Coccidioides immitis RS]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QD5 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 1.9Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CIMG_07932, 4559626 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5501 Coccidioides immitis])</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=3qd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qd5 OCA], [https://pdbe.org/3qd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qd5 RCSB], [https://www.ebi.ac.uk/pdbsum/3qd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qd5 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6] </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=3qd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qd5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qd5 RCSB], [http://www.ebi.ac.uk/pdbsum/3qd5 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RPIB_COCIM RPIB_COCIM] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 17: |
Line 18: |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3qd5" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Coccidioides immitis]] | + | [[Category: Coccidioides immitis RS]] |
| - | [[Category: Ribose-5-phosphate isomerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Coccidioidomycosis]]
| + | |
| - | [[Category: Hypothetical protein]]
| + | |
| - | [[Category: Iodide ion]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Putative uncharacterized protein]]
| + | |
| - | [[Category: Ssgcid]]
| + | |
| Structural highlights
Function
RPIB_COCIM
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
|
