1g1a: Difference between revisions

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<StructureSection load='1g1a' size='340' side='right'caption='[[1g1a]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
<StructureSection load='1g1a' size='340' side='right'caption='[[1g1a]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1g1a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G1A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1G1A FirstGlance]. <br>
<table><tr><td colspan='2'>[[1g1a]] is a 4 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=1G1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G1A FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.47&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RMLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g1a OCA], [https://pdbe.org/1g1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g1a RCSB], [https://www.ebi.ac.uk/pdbsum/1g1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g1a ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1g1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g1a OCA], [http://pdbe.org/1g1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g1a RCSB], [http://www.ebi.ac.uk/pdbsum/1g1a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1g1a ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RMLB_SALTY RMLB_SALTY]] Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction.<ref>PMID:11796113</ref> 
[https://www.uniprot.org/uniprot/Q9EU31_SALER Q9EU31_SALER]  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1g1a ConSurf].
</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=1g1a ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
l-Rhamnose is a 6-deoxyhexose that is found in a variety of different glycoconjugates in the cell walls of pathogenic bacteria. The precursor of l-rhamnose is dTDP-l-rhamnose, which is synthesised from glucose- 1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway requiring four enzymes. Significantly this pathway does not exist in humans and all four enzymes therefore represent potential therapeutic targets. dTDP-D-glucose 4,6-dehydratase (RmlB; EC 4.2.1.46) is the second enzyme in the dTDP-L-rhamnose biosynthetic pathway. The structure of Salmonella enterica serovar Typhimurium RmlB had been determined to 2.47 A resolution with its cofactor NAD(+) bound. The structure has been refined to a crystallographic R-factor of 20.4 % and an R-free value of 24.9 % with good stereochemistry.RmlB functions as a homodimer with monomer association occurring principally through hydrophobic interactions via a four-helix bundle. Each monomer exhibits an alpha/beta structure that can be divided into two domains. The larger N-terminal domain binds the nucleotide cofactor NAD(+) and consists of a seven-stranded beta-sheet surrounded by alpha-helices. The smaller C-terminal domain is responsible for binding the sugar substrate dTDP-d-glucose and contains four beta-strands and six alpha-helices. The two domains meet to form a cavity in the enzyme. The highly conserved active site Tyr(167)XXXLys(171) catalytic couple and the GlyXGlyXXGly motif at the N terminus characterise RmlB as a member of the short-chain dehydrogenase/reductase extended family.The quaternary structure of RmlB and its similarity to a number of other closely related short-chain dehydrogenase/reductase enzymes have enabled us to propose a mechanism of catalysis for this important enzyme.
The crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-l-rhamnose pathway.,Allard ST, Giraud MF, Whitfield C, Graninger M, Messner P, Naismith JH J Mol Biol. 2001 Mar 16;307(1):283-95. PMID:11243820<ref>PMID:11243820</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1g1a" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[DTDP-glucose 4%2C6-dehydratase|DTDP-glucose 4%2C6-dehydratase]]
*[[DTDP-glucose 4%2C6-dehydratase|DTDP-glucose 4%2C6-dehydratase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus typhimurium loeffler 1892]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: DTDP-glucose 4,6-dehydratase]]
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
[[Category: Allard, S T.M]]
[[Category: Allard STM]]
[[Category: Giraud, M F]]
[[Category: Giraud M-F]]
[[Category: Graninger, M]]
[[Category: Graninger M]]
[[Category: Messner, P]]
[[Category: Messner P]]
[[Category: Naismith, J H]]
[[Category: Naismith JH]]
[[Category: Whitfield, C]]
[[Category: Whitfield C]]
[[Category: Lyase]]
[[Category: Protein-nad complex]]
[[Category: Rossmann fold]]
[[Category: Short chain dehydrogenase]]

Latest revision as of 10:21, 7 February 2024

THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB)FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUMTHE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB)FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM

Structural highlights

1g1a is a 4 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 2.47Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9EU31_SALER

Evolutionary Conservation

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

See Also

1g1a, resolution 2.47Å

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