3jyo: Difference between revisions

Latest revision as of 08:06, 6 September 2023

Quinate dehydrogenase from Corynebacterium glutamicum in complex with NAD

Structural highlights

3jyo is a 1 chain structure with sequence from Corynebacterium glutamicum ATCC 13032. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1Å
Ligands:	NAD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AROE_CORGL Catalyzes the NAD(+)-dependent oxidation of both quinate and shikimate to 3-dehydroquinate and 3-dehydroshikimate, respectively. Seems to play a key role in the quinate degradation pathway.^[1]

Publication Abstract from PubMed

Abstract Quinate dehydrogenase (QDH) catalyzes the reversible oxidation of quinate to 3-dehydroquinate by NADH and is involved in the catabolic quinate metabolism required for the degradation of lignin. The enzyme is a member of the family of shikimate/quinate dehydrogenases (SDH/QDH) occurring in bacteria and plants. We characterized the dual-substrate quinate/shikimate dehydrogenase QSDH from Corynebacterium glutamicum (CglQSDH) kinetically and revealed a clear substrate preference of CglQSDH for quinate compared to shikimate both at the pH-optimum and in a physiological pH-range, which is a remarkable contrast to closely related SDH/QDH enzymes. With respect to the cosubstrate CglQSDH is strictly NAD(H) dependent. These substrate and cosubstrate profiles correlate nicely to the details of three atomic resolution crystal structures of CglQSDH in different functional states we report here: with bound NAD+ (binary complex) and as ternary complexes with NADH plus either shikimate or quinate. The CglQSDH-NADH-quinate structure is the first complex structure of any member of the SDH/QDH family with quinate. Based on this novel structural information and systematic sequence and structure comparisons with closely related enzymes we can explain the strict NAD(H) dependency of CglQSDH as well as its discrimination between shikimate and quinate.

Enzyme-substrate complexes of the quinate/shikimate dehydrogenase from Corynebacterium glutamicum enable new insights in substrate and cofactor binding, specificity and discrimination.,Hoppner A, Schomburg D, Niefind K Biol Chem. 2013 Aug 8. pii:, /j/bchm.just-accepted/hsz-2013-0170/hsz-2013-0170.xml. doi:, 10.1515/hsz-2013-0170. PMID:23929881^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Schoepe J, Niefind K, Schomburg D. 1.6 angstroms structure of an NAD+-dependent quinate dehydrogenase from Corynebacterium glutamicum. Acta Crystallogr D Biol Crystallogr. 2008 Jul;D64(Pt 7):803-9. Epub 2008, Jun 18. PMID:18566515 doi:https://dx.doi.org/10.1107/S090744490801411X
↑ Hoppner A, Schomburg D, Niefind K. Enzyme-substrate complexes of the quinate/shikimate dehydrogenase from Corynebacterium glutamicum enable new insights in substrate and cofactor binding, specificity and discrimination. Biol Chem. 2013 Aug 8. pii:, /j/bchm.just-accepted/hsz-2013-0170/hsz-2013-0170.xml. doi:, 10.1515/hsz-2013-0170. PMID:23929881 doi:10.1515/hsz-2013-0170

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Schoepe J, Niefind K, Schomburg D. 1.6 angstroms structure of an NAD+-dependent quinate dehydrogenase from Corynebacterium glutamicum. Acta Crystallogr D Biol Crystallogr. 2008 Jul;D64(Pt 7):803-9. Epub 2008, Jun 18. PMID:18566515 doi:https://dx.doi.org/10.1107/S090744490801411X

[2] Hoppner A, Schomburg D, Niefind K. Enzyme-substrate complexes of the quinate/shikimate dehydrogenase from Corynebacterium glutamicum enable new insights in substrate and cofactor binding, specificity and discrimination. Biol Chem. 2013 Aug 8. pii:, /j/bchm.just-accepted/hsz-2013-0170/hsz-2013-0170.xml. doi:, 10.1515/hsz-2013-0170. PMID:23929881 doi:10.1515/hsz-2013-0170

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='3jyo' size='340' side='right'caption='[[3jyo]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3jyo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corgl Corgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JYO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3jyo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JYO FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
+</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nlo|2nlo]], [[3jyp|3jyp]], [[3jyq|3jyq]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aroE, cg0504, Cgl0424 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 CORGL])</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=3jyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jyo OCA], [https://pdbe.org/3jyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jyo RCSB], [https://www.ebi.ac.uk/pdbsum/3jyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jyo ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/AROE_CORGL AROE_CORGL]] Catalyzes the NAD(+)-dependent oxidation of both quinate and shikimate to 3-dehydroquinate and 3-dehydroshikimate, respectively. Seems to play a key role in the quinate degradation pathway.<ref>PMID:18566515</ref>
+[https://www.uniprot.org/uniprot/AROE_CORGL AROE_CORGL] Catalyzes the NAD(+)-dependent oxidation of both quinate and shikimate to 3-dehydroquinate and 3-dehydroshikimate, respectively. Seems to play a key role in the quinate degradation pathway.<ref>PMID:18566515</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Corgl]]
+[[Category: Corynebacterium glutamicum ATCC 13032]]
 [[Category: Large Structures]]
-[[Category: Hoeppner, A]]
+[[Category: Hoeppner A]]
-[[Category: Niefind, K]]
+[[Category: Niefind K]]
-[[Category: Schomburg, D]]
+[[Category: Schomburg D]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Aromatic amino acid biosynthesis]]
-[[Category: Enzyme-cofactor complex]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]

3jyo: Difference between revisions

Latest revision as of 08:06, 6 September 2023

Quinate dehydrogenase from Corynebacterium glutamicum in complex with NAD

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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