5kka: Difference between revisions
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==E. coli malate dehydrogenase with the inhibitor 6DHNAD== | |||
<StructureSection load='5kka' size='340' side='right' caption='[[5kka]], [[Resolution|resolution]] 1.75Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5kka]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KKA FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6V0:[[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+hydrogen+phosphate'>6V0</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5kkc|5kkc]]</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] </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=5kka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kka OCA], [http://pdbe.org/5kka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kka RCSB], [http://www.ebi.ac.uk/pdbsum/5kka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kka ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/MDH_ECOLI MDH_ECOLI]] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_01516] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Renalase catalyzes the oxidation of isomers of beta-NAD(P)H that carry the hydride in the 2 or 6 positions of the nicotinamide base to form beta-NAD(P)+. This activity is thought to alleviate inhibition of multiple beta-NAD(P)-dependent enzymes of primary and secondary metabolism by these isomers. Here we present evidence for a variety of ligand binding phenomena relevant to the function of renalase. We offer evidence of the potential for primary metabolism inhibition with structures of malate dehydrogenase and lactate dehydrogenase bound to the 6-dihydroNAD isomer. The previously observed preference of renalase from Pseudomonas for NAD-derived substrates over those derived from NADP is accounted for by the structure of the enzyme in complex with NADPH. We also show that nicotinamide nucleosides and mononucleotides reduced in the 2- and 6-positions are renalase substrates, but bind weakly. A seven-fold enhancement of acquisition (kred/Kd) for 6-dihydronicotinamide riboside was observed for human renalase in the presence of ADP. However, generally the addition of complement ligands, AMP for mononucleotide or ADP for nucleoside substrates, did not enhance the reductive half-reaction. Non-substrate nicotinamide nucleosides or nucleotides bind weakly suggesting that only beta-NADH and beta-NADPH compete with dinucleotide substrates for access to the active site. | |||
Ligand binding phenomena that pertain to the metabolic function of renalase.,Beaupre BA, Roman JV, Hoag MR, Meneely KM, Silvaggi NR, Lamb AL, Moran GR Arch Biochem Biophys. 2016 Oct 18;612:46-56. doi: 10.1016/j.abb.2016.10.011. PMID:27769837<ref>PMID:27769837</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Lamb, A | <div class="pdbe-citations 5kka" style="background-color:#fffaf0;"></div> | ||
[[Category: Meneely, K | == References == | ||
[[Category: Moran, G | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Malate dehydrogenase]] | |||
[[Category: Lamb, A L]] | |||
[[Category: Meneely, K M]] | |||
[[Category: Moran, G R]] | |||
[[Category: Beta- 6-dihydronicotimide adenine dinucleotide]] | |||
[[Category: Dehydrogenase]] | |||
[[Category: Inhibitor]] | |||
[[Category: Malate]] | |||
[[Category: Oxidoreductase]] | |||
Revision as of 21:17, 2 November 2016
E. coli malate dehydrogenase with the inhibitor 6DHNADE. coli malate dehydrogenase with the inhibitor 6DHNAD
Structural highlights
Function[MDH_ECOLI] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_01516] Publication Abstract from PubMedRenalase catalyzes the oxidation of isomers of beta-NAD(P)H that carry the hydride in the 2 or 6 positions of the nicotinamide base to form beta-NAD(P)+. This activity is thought to alleviate inhibition of multiple beta-NAD(P)-dependent enzymes of primary and secondary metabolism by these isomers. Here we present evidence for a variety of ligand binding phenomena relevant to the function of renalase. We offer evidence of the potential for primary metabolism inhibition with structures of malate dehydrogenase and lactate dehydrogenase bound to the 6-dihydroNAD isomer. The previously observed preference of renalase from Pseudomonas for NAD-derived substrates over those derived from NADP is accounted for by the structure of the enzyme in complex with NADPH. We also show that nicotinamide nucleosides and mononucleotides reduced in the 2- and 6-positions are renalase substrates, but bind weakly. A seven-fold enhancement of acquisition (kred/Kd) for 6-dihydronicotinamide riboside was observed for human renalase in the presence of ADP. However, generally the addition of complement ligands, AMP for mononucleotide or ADP for nucleoside substrates, did not enhance the reductive half-reaction. Non-substrate nicotinamide nucleosides or nucleotides bind weakly suggesting that only beta-NADH and beta-NADPH compete with dinucleotide substrates for access to the active site. Ligand binding phenomena that pertain to the metabolic function of renalase.,Beaupre BA, Roman JV, Hoag MR, Meneely KM, Silvaggi NR, Lamb AL, Moran GR Arch Biochem Biophys. 2016 Oct 18;612:46-56. doi: 10.1016/j.abb.2016.10.011. PMID:27769837[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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