This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2nlo

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 19:25, 25 December 2014

Crystal Structure of the Quinate Dehydrogenase from Corynebacterium glutamicum

Structural highlights

2nlo is a 1 chain structure with sequence from Corgl. This structure supersedes the now removed PDB entry 2ez3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	Cgl0424 (CORGL)
Activity:	Shikimate dehydrogenase, with EC number 1.1.1.25
Resources:	FirstGlance, OCA, RCSB, PDBsum

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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

To date, three different functional classes of bacterial shikimate/quinate dehydrogenases have been identified and are referred to as AroE, SDH-L and YdiB. The enzyme AroE and the catalytically much slower SDH-L clearly prefer NADP+/NADPH as the cosubstrate and are specific for (dehydro-)shikimate, whereas in YdiB the differences in affinity for NADP+/NADPH versus NAD+/NADH as well as for (dehydro-)shikimate versus (dehydro-)quinate are marginal. These three subclasses have a similar three-dimensional fold and hence all belong to the same structural class of proteins. In this paper, the crystal structure of an enzyme from Corynebacterium glutamicum is presented that clearly prefers NAD+ as a cosubstrate and that demonstrates a higher catalytic efficiency for quinate rather than shikimate. While the kinetic constants for this enzyme clearly differ from those reported for AroE, SDH-L and YdiB, the three-dimensional structure of this protein is similar to members of these three subclasses. Thus, the enzyme described here belongs to a new functional class of the shikimate/quinate dehydrogenase family. The different substrate and cosubstrate specificities of this enzyme relative to all other known bacterial shikimate/quinate dehydrogenases are discussed by means of analyzing the crystal structure and derived models. It is proposed that in contrast to shikimate, quinate forms a hydrogen bond to the NAD+. In addition, it is suggested that the hydroxyl group of a conserved active-site threonine hydrogen bonds to quinate more effectively than to shikimate. Also, the hydroxyl group of a conserved tyrosine approaches the carboxylate group of quinate more closely than it does the carboxylate group of shikimate. Taken together, these factors most likely lead to a lower Michaelis constant and therefore to a higher catalytic efficiency for quinate. The active site of the dehydrogenase reported here is larger than those of other known shikimate/quinate dehydrogenases, which may explain why quinate is easily accommodated within the catalytic cleft.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2nlo"

@@ Line 2: / Line 2: @@
 <StructureSection load='2nlo' size='340' side='right' caption='[[2nlo]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2nlo]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2ez3 2ez3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NLO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NLO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2nlo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corgl Corgl]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2ez3 2ez3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NLO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NLO FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cgl0424 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 CORGL])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </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=2nlo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nlo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nlo RCSB], [http://www.ebi.ac.uk/pdbsum/2nlo PDBsum]</span></td></tr>
 </table>
+== Function ==
+[[http://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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 35: @@
 __TOC__
 </StructureSection>
+[[Category: Corgl]]
 [[Category: Shikimate dehydrogenase]]
 [[Category: Niefind, K]]

2nlo

From Proteopedia

Revision as of 19:25, 25 December 2014

Crystal Structure of the Quinate Dehydrogenase from Corynebacterium glutamicum

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox