Proteopedia

1kc1: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1kc1.jpg|left|200px]]


{{Structure
==Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH==
|PDB= 1kc1 |SIZE=350|CAPTION= <scene name='initialview01'>1kc1</scene>, resolution 2.60&Aring;
<StructureSection load='1kc1' size='340' side='right'caption='[[1kc1]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
<table><tr><td colspan='2'>[[1kc1]] 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=1KC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KC1 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]] 2.6&#8491;</td></tr>
|GENE= rfbA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=602 Salmonella 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=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1kc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc1 OCA], [https://pdbe.org/1kc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1kc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kc1 ProSAT]</span></td></tr>
|RELATEDENTRY=[[1kbz|1KBZ]], [[1kc0|1KC0]], [[1kc3|1KC3]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc1 OCA], [http://www.ebi.ac.uk/pdbsum/1kc1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kc1 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 NADPH'''
[[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/kc/1kc1_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>
1KC1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC1 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=1kc1 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 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 21:46:20 2008''

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/w/1kc1"