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[[Image:1n2s.jpg|left|200px]]


{{Structure
==CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH==
|PDB= 1n2s |SIZE=350|CAPTION= <scene name='initialview01'>1n2s</scene>, resolution 2.00&Aring;
<StructureSection load='1n2s' size='340' side='right'caption='[[1n2s]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
<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>
|ACTIVITY= <span class='plainlinks'>[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] </span>
</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>
|GENE= RFBA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])
<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>
|DOMAIN=
<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>
|RELATEDENTRY=[[1kbz|1KBZ]], [[1kc1|1KC1]], [[1kc3|1KC3]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2s OCA], [http://www.ebi.ac.uk/pdbsum/1n2s PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1n2s RCSB]</span>
== Function ==
}}
[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.
 
== Evolutionary Conservation ==
'''CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n2/1n2s_consurf.spt"</scriptWhenChecked>
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.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
1N2S is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. This structure supersedes the now removed PDB entry 1KC0. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2S OCA].  
</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].
 
<div style="clear:both"></div>
==Reference==
__TOC__
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://www.ncbi.nlm.nih.gov/pubmed/12057193 12057193]
</StructureSection>
[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
[[Category: dTDP-4-dehydrorhamnose reductase]]
[[Category: Blankenfeldt W]]
[[Category: Blankenfeldt, W.]]
[[Category: Giraud MF]]
[[Category: Giraud, M F.]]
[[Category: Graninger M]]
[[Category: Graninger, M.]]
[[Category: Kerr ID]]
[[Category: Kerr, I D.]]
[[Category: Leonard GA]]
[[Category: Leonard, G A.]]
[[Category: Mcmiken HJ]]
[[Category: Mcmiken, H J.]]
[[Category: Messner P]]
[[Category: Messner, P.]]
[[Category: Naismith JH]]
[[Category: Naismith, J H.]]
[[Category: Whitfield C]]
[[Category: Whitfield, C.]]
[[Category: rossman-fold]]
[[Category: sugar-nucleotide-binding domain]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:24:34 2008''

Latest revision as of 10:51, 14 February 2024

CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADHCRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH

Structural highlights

1n2s is a 1 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium. This structure supersedes the now removed PDB entry 1kc0. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
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.

1n2s, resolution 2.00Å

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