1dzt

From Proteopedia

(Difference between revisions)

Current revision

RMLC FROM SALMONELLA TYPHIMURIUM

Structural highlights

1dzt is a 2 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 2.2Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RMLC_SALTY Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.^[1]

Evolutionary Conservation

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

Publication Abstract from PubMed

Deoxythymidine diphosphate (dTDP)-L-rhamnose is the precursor of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. dTDP-L-rhamnose is synthesized from glucose-1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway involving four distinct enzymes. This pathway does not exist in humans and the enzymes involved in dTDP-L-rhamnose synthesis are potential targets for the design of new therapeutic agents. Here, the crystal structure of dTDP-6-deoxy-D-xylo-4-hexulose 3,5 epimerase (RmlC, EC5.1.3.13) from Salmonella enterica serovar Typhimurium was determined. The third enzyme of the rhamnose biosynthetic pathway, RmlC epimerizes at two carbon centers, the 3 and 5 positions of the sugar ring. The structure was determined by multiwavelength anomalous diffraction to a resolution of 2.17 A. RmlC is a dimer and each monomer is formed mainly from two beta-sheets arranged in a beta-sandwich. The structure of a dTDP-phenol-RmlC complex shows the substrate-binding site to be located between the two beta-sheets; this site is formed from residues of both monomers. Sequence alignments of other RmlC enzymes confirm that this region is very highly conserved. The enzyme is distinct structurally from other epimerases known and thus, is the first example of a new class of carbohydrate epimerase.

RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase.,Giraud MF, Leonard GA, Field RA, Berlind C, Naismith JH Nat Struct Biol. 2000 May;7(5):398-402. PMID:10802738^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Dong C, Major LL, Srikannathasan V, Errey JC, Giraud MF, Lam JS, Graninger M, Messner P, McNeil MR, Field RA, Whitfield C, Naismith JH. RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation. J Mol Biol. 2007 Jan 5;365(1):146-59. Epub 2006 Sep 29. PMID:17046787 doi:http://dx.doi.org/10.1016/j.jmb.2006.09.063
↑ Giraud MF, Leonard GA, Field RA, Berlind C, Naismith JH. RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase. Nat Struct Biol. 2000 May;7(5):398-402. PMID:10802738 doi:10.1038/75178

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dzt"

Categories: Large Structures | Salmonella enterica subsp. enterica serovar Typhimurium | Giraud MF | Naismith JH

@@ Line 3: / Line 3: @@
 <StructureSection load='1dzt' size='340' side='right'caption='[[1dzt]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dzt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DZT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dzt]] is a 2 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=1DZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DZT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATY:3-O-ACETYLTHYMIDINE-5-DIPHOSPHATE'>ATY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TPE:3-O-ACETYLTHYMIDINE-(5+DIPHOSPHATE+PHENYL+ESTER)'>TPE</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]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dzr|1dzr]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATY:3-O-ACETYLTHYMIDINE-5-DIPHOSPHATE'>ATY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TPE:3-O-ACETYLTHYMIDINE-(5+DIPHOSPHATE+PHENYL+ESTER)'>TPE</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_3,5-epimerase dTDP-4-dehydrorhamnose 3,5-epimerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.13 5.1.3.13] </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=1dzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dzt OCA], [https://pdbe.org/1dzt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dzt RCSB], [https://www.ebi.ac.uk/pdbsum/1dzt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dzt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RMLC_SALTY RMLC_SALTY]] Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.<ref>PMID:17046787</ref>
+[https://www.uniprot.org/uniprot/RMLC_SALTY RMLC_SALTY] Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.<ref>PMID:17046787</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 37: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: DTDP-4-dehydrorhamnose 3,5-epimerase]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: Giraud, M F]]
+[[Category: Giraud MF]]
-[[Category: Naismith, J H]]
+[[Category: Naismith JH]]
-[[Category: 3\]]
-[[Category: Hexulose epimerase]]
-[[Category: Isomerase]]

1dzt

From Proteopedia

Current revision

RMLC FROM SALMONELLA TYPHIMURIUM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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