4g3m
From Proteopedia
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| - | [[ | + | ==Complex Structure of Bacillus subtilis RibG: The Deamination Process in Riboflavin Biosynthesis== |
| + | <StructureSection load='4g3m' size='340' side='right' caption='[[4g3m]], [[Resolution|resolution]] 2.56Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4g3m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G3M FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AI9:[(2R,3S,4S,5E)-5-[[5-AZANYL-2,4-BIS(OXIDANYLIDENE)-1H-PYRIMIDIN-6-YL]IMINO]-2,3,4-TRIS(OXIDANYL)PENTYL]+DIHYDROGEN+PHOSPHATE'>AI9</scene>, <scene name='pdbligand=AOF:N-(5-AMINO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAMINE'>AOF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2b3z|2b3z]], [[3ex8|3ex8]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU23280, ribD, ribG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 Bacillus subtilis subsp. subtilis str. 168])</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=4g3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g3m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g3m RCSB], [http://www.ebi.ac.uk/pdbsum/4g3m PDBsum]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Eubacterial RibG and yeast Rib2 possess a deaminase domain for pyrimidine deamination in the second and third steps, respectively, of riboflavin biosynthesis. These enzymes are specific for ribose and ribitol, respectively. Here, the crystal structure of Bacillus subtilis RibG in complex with a deaminase product is reported at 2.56 A resolution. Two loops move towards the product on substrate binding, resulting in interactions with the ribosyl and phosphate groups and significant conformational changes. The product carbonyl moiety is bent out of the pyrimidine ring to coordinate to the catalytic zinc ion. Such distortions in the bound substrate and product may play an essential role in enzyme catalysis. The yeast Rib2 structure was modelled and a mutational analysis was carried out in order to understand the mechanism of substrate recognition in these two enzymes. Detailed structural comparisons revealed that the two consecutive carbonyl backbones that occur prior to the PCXXC signature constitute a binding hole for the target amino group of the substrate. This amino-binding hole is essential in B. subtilis RibG and is also conserved in the RNA/DNA-editing deaminases. | ||
| - | + | Evolution of vitamin B(2) biosynthesis: eubacterial RibG and fungal Rib2 deaminases.,Chen SC, Shen CY, Yen TM, Yu HC, Chang TH, Lai WL, Liaw SH Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):227-36. doi:, 10.1107/S0907444912044903. Epub 2013 Jan 19. PMID:23385458<ref>PMID:23385458</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | == | + | __TOC__ |
| - | + | </StructureSection> | |
[[Category: Bacillus subtilis subsp. subtilis str. 168]] | [[Category: Bacillus subtilis subsp. subtilis str. 168]] | ||
| - | [[Category: Chang, T H | + | [[Category: Chang, T H]] |
| - | [[Category: Chen, S C | + | [[Category: Chen, S C]] |
| - | [[Category: Lai, W L | + | [[Category: Lai, W L]] |
| - | [[Category: Liaw, S H | + | [[Category: Liaw, S H]] |
| - | [[Category: Shen, C Y | + | [[Category: Shen, C Y]] |
| - | [[Category: Yen, T M | + | [[Category: Yen, T M]] |
| - | [[Category: Yu, H C | + | [[Category: Yu, H C]] |
[[Category: Alpha/beta/alpha]] | [[Category: Alpha/beta/alpha]] | ||
[[Category: Deaminase domain]] | [[Category: Deaminase domain]] | ||
Revision as of 17:07, 9 December 2014
Complex Structure of Bacillus subtilis RibG: The Deamination Process in Riboflavin Biosynthesis
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