1n2s: Difference between revisions

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New page: left|200px<br /><applet load="1n2s" size="450" color="white" frame="true" align="right" spinBox="true" caption="1n2s, resolution 2.00Å" /> '''CRYSTAL STRUCTURE OF...
 
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[[Image:1n2s.jpg|left|200px]]<br /><applet load="1n2s" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1n2s, resolution 2.00&Aring;" />
'''CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH'''<br />


==Overview==
==CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH==
dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) catalyzes the final step, in the conversion of dTDP-D-glucose to dTDP-L-rhamnose in an NAD(P)H- and, Mg2+-dependent reaction. L-rhamnose biosynthesis is an antibacterial, target. The structure of RmlD from Salmonella enterica serovar Typhimurium, has been determined, and complexes with NADH, NADPH, and dTDP-L-rhamnose, are reported. RmlD differs from other short chain dehydrogenases in that, it has a novel dimer interface that contains Mg2+. Enzyme catalysis, involves hydride transfer from the nicotinamide ring of the cofactor to, the C4'-carbonyl group of the substrate. The substrate is activated, through protonation by a conserved tyrosine. NAD(P)H is bound in a, solvent-exposed cleft, allowing facile replacement. We suggest a novel, role for the conserved serine/threonine residue of the catalytic triad of, SDR enzymes.
<StructureSection load='1n2s' size='340' side='right'caption='[[1n2s]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1n2s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc0 1kc0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N2S FirstGlance]. <br>
1N2S is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium] with MG, NAD and TRS as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1KC0. Active as [http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N2S 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]] 2&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [https://pdbe.org/1n2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB], [https://www.ebi.ac.uk/pdbsum/1n2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2s ProSAT]</span></td></tr>
Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode., Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH, Structure. 2002 Jun;10(6):773-86. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12057193 12057193]
</table>
[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
== Function ==
[[Category: Single protein]]
[https://www.uniprot.org/uniprot/RMLD_SALTY RMLD_SALTY] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.
[[Category: dTDP-4-dehydrorhamnose reductase]]
== Evolutionary Conservation ==
[[Category: Blankenfeldt, W.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Giraud, M.F.]]
Check<jmol>
[[Category: Graninger, M.]]
  <jmolCheckbox>
[[Category: Kerr, I.D.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n2/1n2s_consurf.spt"</scriptWhenChecked>
[[Category: Leonard, G.A.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Mcmiken, H.J.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: Messner, P.]]
  </jmolCheckbox>
[[Category: Naismith, J.H.]]
</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=1n2s ConSurf].
[[Category: Whitfield, C.]]
<div style="clear:both"></div>
[[Category: MG]]
__TOC__
[[Category: NAD]]
</StructureSection>
[[Category: TRS]]
[[Category: Large Structures]]
[[Category: rossman-fold]]
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
[[Category: sugar-nucleotide-binding domain]]
[[Category: Blankenfeldt W]]
 
[[Category: Giraud MF]]
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:54:04 2007''
[[Category: Graninger M]]
[[Category: Kerr ID]]
[[Category: Leonard GA]]
[[Category: Mcmiken HJ]]
[[Category: Messner P]]
[[Category: Naismith JH]]
[[Category: Whitfield C]]
Retrieved from "https://proteopedia.org/1n2s"