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[[Image:1kc3.jpg|left|200px]]<br /><applet load="1kc3" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1kc3, resolution 2.70&Aring;" />
'''Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose'''<br />


==Overview==
==Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose==
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='1kc3' size='340' side='right'caption='[[1kc3]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1kc3]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KC3 FirstGlance]. <br>
1KC3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=NDP:'>NDP</scene> and <scene name='pdbligand=TRH:'>TRH</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC3 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]] 2.7&#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=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</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=1kc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc3 OCA], [https://pdbe.org/1kc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kc3 RCSB], [https://www.ebi.ac.uk/pdbsum/1kc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kc3 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 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/kc/1kc3_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=1kc3 ConSurf].
[[Category: Whitfield, C.]]
<div style="clear:both"></div>
[[Category: MG]]
__TOC__
[[Category: NDP]]
</StructureSection>
[[Category: TRH]]
[[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://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:32:26 2008''
[[Category: Graninger M]]
[[Category: Kerr ID]]
[[Category: Leonard GA]]
[[Category: McMiken HJ]]
[[Category: Messner P]]
[[Category: Naismith JH]]
[[Category: Whitfield C]]

Latest revision as of 10:45, 7 February 2024

Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnoseCrystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose

Structural highlights

1kc3 is a 1 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

Evolutionary Conservation

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

1kc3, resolution 2.70Å

Drag the structure with the mouse to rotate

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