4z0p: Difference between revisions

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New page: '''Unreleased structure''' The entry 4z0p is ON HOLD Authors: Sroka, P., Gasiorowska, O.A., Handing, K.B., Shabalin, I.G., Porebski, P.J., Hillerich, B.S, Bonanno, J., Almo, S.C., Minor...
 
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'''Unreleased structure'''


The entry 4z0p is ON HOLD
==Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADPH and oxalate==
<StructureSection load='4z0p' size='340' side='right'caption='[[4z0p]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4z0p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti_1021 Sinorhizobium meliloti 1021]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z0P FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=OXD:OXALIC+ACID'>OXD</scene></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=4z0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z0p OCA], [https://pdbe.org/4z0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z0p RCSB], [https://www.ebi.ac.uk/pdbsum/4z0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z0p ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q92T34_RHIME Q92T34_RHIME]
<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.


Authors: Sroka, P., Gasiorowska, O.A., Handing, K.B., Shabalin, I.G., Porebski, P.J., Hillerich, B.S, Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
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>


Description: Crystal structure of NADP-dependent dehydrogenase from Sinorhizobium meliloti in complex with NADPH and oxalate
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Almo, S.C]]
<div class="pdbe-citations 4z0p" style="background-color:#fffaf0;"></div>
[[Category: Porebski, P.J]]
== References ==
[[Category: Minor, W]]
<references/>
[[Category: Handing, K.B]]
__TOC__
[[Category: Shabalin, I.G]]
</StructureSection>
[[Category: Hillerich, B.S, Bonanno, J]]
[[Category: Large Structures]]
[[Category: Sroka, P]]
[[Category: Sinorhizobium meliloti 1021]]
[[Category: New York Structural Genomics Research Consortium (Nysgrc)]]
[[Category: Almo SC]]
[[Category: Gasiorowska, O.A]]
[[Category: Bonanno J]]
[[Category: Gasiorowska OA]]
[[Category: Handing KB]]
[[Category: Hillerich BS]]
[[Category: Minor W]]
[[Category: Porebski PJ]]
[[Category: Shabalin IG]]
[[Category: Sroka P]]
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