1npy: Difference between revisions

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New page: left|200px<br /><applet load="1npy" size="450" color="white" frame="true" align="right" spinBox="true" caption="1npy, resolution 1.75Å" /> '''Structure of shikima...
 
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[[Image:1npy.gif|left|200px]]<br /><applet load="1npy" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1npy, resolution 1.75&Aring;" />
'''Structure of shikimate 5-dehydrogenase-like protein HI0607'''<br />


==Overview==
==Structure of shikimate 5-dehydrogenase-like protein HI0607==
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.
<StructureSection load='1npy' size='340' side='right'caption='[[1npy]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1npy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. 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 [https://proteopedia.org/fgij/fg.htm?mol=1NPY FirstGlance]. <br>
1NPY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae] with ACE as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NPY OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</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>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1npy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1npy OCA], [https://pdbe.org/1npy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1npy RCSB], [https://www.ebi.ac.uk/pdbsum/1npy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1npy ProSAT], [https://www.topsan.org/Proteins/MCSG/1npy TOPSAN]</span></td></tr>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15735308 15735308]
</table>
== Function ==
[https://www.uniprot.org/uniprot/SHDHL_HAEIN SHDHL_HAEIN] In vitro, is able to catalyze the NADP(+)-dependent oxidation of shikimate to 3-dehydroshikimate. However, has much lower activity than classical shikimate dehydrogenases AroE, indicating that shikimate may not be the biological substrate. Cannot utilize NAD(+) instead of NADP(+). Is not able to catalyze the oxidation of quinate.<ref>PMID:15735308</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <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>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1npy ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Collart, F.]]
[[Category: Collart F]]
[[Category: Joachimiak, A.]]
[[Category: Joachimiak A]]
[[Category: Korolev, S.]]
[[Category: Korolev S]]
[[Category: Koroleva, O.]]
[[Category: Koroleva O]]
[[Category: MCSG, Midwest.Center.for.Structural.Genomics.]]
[[Category: Zarembinski T]]
[[Category: Zarembinski, T.]]
[[Category: ACE]]
[[Category: mcsg]]
[[Category: midwest center for structural genomics]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: structural genomics]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:28:37 2007''

Latest revision as of 10:58, 14 February 2024

Structure of shikimate 5-dehydrogenase-like protein HI0607Structure of shikimate 5-dehydrogenase-like protein HI0607

Structural highlights

1npy is a 4 chain structure with sequence from Haemophilus influenzae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.75Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

SHDHL_HAEIN In vitro, is able to catalyze the NADP(+)-dependent oxidation of shikimate to 3-dehydroshikimate. However, has much lower activity than classical shikimate dehydrogenases AroE, indicating that shikimate may not be the biological substrate. Cannot utilize NAD(+) instead of NADP(+). Is not able to catalyze the oxidation of quinate.[1]

Evolutionary Conservation

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

References

  1. ↑ 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

1npy, resolution 1.75Å

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