5v7n
From Proteopedia
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<StructureSection load='5v7n' size='340' side='right' caption='[[5v7n]], [[Resolution|resolution]] 1.75Å' scene=''> | <StructureSection load='5v7n' size='340' side='right' caption='[[5v7n]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5v7n]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5v7n]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7N FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8YV:2-KETO-D-GLUCONIC+ACID'>8YV</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8YV:2-KETO-D-GLUCONIC+ACID'>8YV</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j23|5j23]], [[5uog|5uog]], [[5v6q|5v6q]], [[5v7g|5v7g]], [[5v72|5v72]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j23|5j23]], [[5uog|5uog]], [[5v6q|5v6q]], [[5v7g|5v7g]], [[5v72|5v72]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SMc04462 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxypyruvate_reductase Hydroxypyruvate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.81 1.1.1.81] </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=5v7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7n OCA], [http://pdbe.org/5v7n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7n RCSB], [http://www.ebi.ac.uk/pdbsum/5v7n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7n 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=5v7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7n OCA], [http://pdbe.org/5v7n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7n RCSB], [http://www.ebi.ac.uk/pdbsum/5v7n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7n ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The d-2-hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site. | ||
| + | |||
| + | Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.,Kutner J, Shabalin IG, Matelska D, Handing KB, Gasiorowska O, Sroka P, Gorna MW, Ginalski K, Wozniak K, Minor W Biochemistry. 2018 Jan 26. doi: 10.1021/acs.biochem.7b01137. PMID:29309127<ref>PMID:29309127</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5v7n" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Ensifer meliloti]] | ||
| + | [[Category: Hydroxypyruvate reductase]] | ||
[[Category: Almo, S C]] | [[Category: Almo, S C]] | ||
[[Category: Bonanno, J]] | [[Category: Bonanno, J]] | ||
Revision as of 05:53, 16 May 2018
Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADP and 2-Keto-D-gluconic acid
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Categories: Ensifer meliloti | Hydroxypyruvate reductase | Almo, S C | Bonanno, J | Handing, K B | Kutner, J | Matelska, D | Miks, C D | Minor, W | Structural genomic | Shabalin, I G | Nadp | Nadph-dependent glyoxylate/hydroxypyruvate reductase | Nysgrc | Oxidoreductase | Psi-biology | Sinorhizobium meliloti
