5o3z
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==Crystal structure of Sorbitol-6-Phosphate 2-dehydrogenase SrlD from Erwinia amylovora== | ==Crystal structure of Sorbitol-6-Phosphate 2-dehydrogenase SrlD from Erwinia amylovora== | ||
| - | <StructureSection load='5o3z' size='340' side='right' caption='[[5o3z]], [[Resolution|resolution]] 1.84Å' scene=''> | + | <StructureSection load='5o3z' size='340' side='right'caption='[[5o3z]], [[Resolution|resolution]] 1.84Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5o3z]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O3Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O3Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5o3z]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Erwac Erwac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O3Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O3Z FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">srlD, EAMY_3073 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=665029 ERWAC])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sorbitol-6-phosphate_2-dehydrogenase Sorbitol-6-phosphate 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.140 1.1.1.140] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sorbitol-6-phosphate_2-dehydrogenase Sorbitol-6-phosphate 2-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.140 1.1.1.140] </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=5o3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o3z OCA], [http://pdbe.org/5o3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o3z RCSB], [http://www.ebi.ac.uk/pdbsum/5o3z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o3z 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=5o3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o3z OCA], [http://pdbe.org/5o3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o3z RCSB], [http://www.ebi.ac.uk/pdbsum/5o3z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o3z ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Sorbitol-6-phosphate 2-dehydrogenases (S6PDH) catalyze the interconversion of d-sorbitol 6-phosphate to d-fructose 6-phosphate. In the plant pathogen Erwinia amylovora the S6PDH SrlD is used by the bacterium to utilize sorbitol, which is used for carbohydrate transport in the host plants belonging to the Amygdaloideae subfamily (e.g., apple, pear, and quince). We have determined the crystal structure of S6PDH SrlD at 1.84A resolution, which is the first structure of an EC 1.1.1.140 enzyme. Kinetic data show that SrlD is much faster at oxidizing d-sorbitol 6-phosphate than in reducing d-fructose 6-phosphate, however, equilibrium analysis revealed that only part of the d-sorbitol 6-phosphate present in the in vitro environment is converted into d-fructose 6-phosphate. The comparison of the structures of SrlD and Rhodobacter sphaeroides sorbitol dehydrogenase showed that the tetrameric quaternary structure, the catalytic residues and a conserved aspartate residue that confers specificity for NAD(+) over NADP(+) are preserved. Analysis of the SrlD cofactor and substrate binding sites identified residues important for the formation of the complex with cofactor and substrate and in particular the role of Lys42 in selectivity towards the phospho-substrate. The comparison of SrlD backbone with the backbone of 302 short-chain dehydrogenases/reductases showed the conservation of the protein core and identified the variable parts. The SrlD sequence was compared with 500 S6PDH sequences selected by homology revealing that the C-terminal part is more conserved than the N-terminal, the consensus of the catalytic tetrad (Y[SN]AGXA) and a not previously described consensus for the NAD(H) binding. | ||
| + | |||
| + | Structural and functional analysis of Erwinia amylovora SrlD. The first crystal structure of a sorbitol-6-phosphate 2-dehydrogenase.,Salomone-Stagni M, Bartho JD, Kalita E, Rejzek M, Field RA, Bellini D, Walsh MA, Benini S J Struct Biol. 2018 Aug;203(2):109-119. doi: 10.1016/j.jsb.2018.03.010. Epub 2018, Mar 29. PMID:29605571<ref>PMID:29605571</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5o3z" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Erwac]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: Sorbitol-6-phosphate 2-dehydrogenase]] | [[Category: Sorbitol-6-phosphate 2-dehydrogenase]] | ||
[[Category: Bartho, J D]] | [[Category: Bartho, J D]] | ||
Revision as of 07:19, 26 June 2019
Crystal structure of Sorbitol-6-Phosphate 2-dehydrogenase SrlD from Erwinia amylovora
| |||||||||||
