1npy

From Proteopedia

(Difference between revisions)

Revision as of 08:55, 2 December 2020

Structure of shikimate 5-dehydrogenase-like protein HI0607

Structural highlights

1npy is a 4 chain structure with sequence from "bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	HI0607 ("Bacterium influenzae" Lehmann and Neumann 1896)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[Y607_HAEIN] The physiological substrate is not known. Has much lower activity towards shikimate than AroE.

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 two classes of shikimate dehydrogenases have been identified and characterized, YdiB and AroE. YdiB is a bifunctional enzyme that catalyzes the reversible reductions of dehydroquinate to quinate and dehydroshikimate to shikimate in the presence of either NADH or NADPH. In contrast, AroE catalyzes the reversible reduction of dehydroshikimate to shikimate in the presence of NADPH. Here we report the crystal structure and biochemical characterization of HI0607, a novel class of shikimate dehydrogenase annotated as shikimate dehydrogenase-like. The kinetic properties of HI0607 are remarkably different from those of AroE and YdiB. In comparison with YdiB, HI0607 catalyzes the oxidation of shikimate but not quinate. The turnover rate for the oxidation of shikimate is approximately 1000-fold lower compared with that of AroE. Phylogenetic analysis reveals three independent clusters representing three classes of shikimate dehydrogenases, namely AroE, YdiB, and this newly characterized shikimate dehydrogenase-like protein. In addition, mutagenesis studies of two invariant residues, Asp-103 and Lys-67, indicate that they are important catalytic groups that may function as a catalytic pair in the shikimate dehydrogenase reaction. This is the first study that describes the crystal structure as well as mutagenesis and mechanistic analysis of this new class of shikimate dehydrogenase.

Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae.,Singh S, Korolev S, Koroleva O, Zarembinski T, Collart F, Joachimiak A, Christendat D J Biol Chem. 2005 Apr 29;280(17):17101-8. Epub 2005 Feb 25. PMID:15735308^[1]

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

References

↑ Singh S, Korolev S, Koroleva O, Zarembinski T, Collart F, Joachimiak A, Christendat D. Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae. J Biol Chem. 2005 Apr 29;280(17):17101-8. Epub 2005 Feb 25. PMID:15735308 doi:10.1074/jbc.M412753200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://proteopedia.org/wiki/index.php/1npy"

@@ Line 1: / Line 1: @@
 ==Structure of shikimate 5-dehydrogenase-like protein HI0607==
-<StructureSection load='1npy' size='340' side='right' caption='[[1npy]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='1npy' size='340' side='right'caption='[[1npy]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1npy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NPY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1npy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NPY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NPY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HI0607 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=1npy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1npy OCA], [http://pdbe.org/1npy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1npy RCSB], [http://www.ebi.ac.uk/pdbsum/1npy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1npy ProSAT], [http://www.topsan.org/Proteins/MCSG/1npy TOPSAN]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1npy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1npy OCA], [http://pdbe.org/1npy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1npy RCSB], [http://www.ebi.ac.uk/pdbsum/1npy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1npy ProSAT], [http://www.topsan.org/Proteins/MCSG/1npy TOPSAN]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/np/1npy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/np/1npy_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Bacterium influenzae lehmann and neumann 1896]]
+[[Category: Large Structures]]
 [[Category: Collart, F]]
 [[Category: Joachimiak, A]]

1npy

From Proteopedia

Revision as of 08:55, 2 December 2020

Structure of shikimate 5-dehydrogenase-like protein HI0607

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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