1dzt

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:09, 6 December 2023) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dzt.jpg|left|200px]]
 
-
{{Structure
+
==RMLC FROM SALMONELLA TYPHIMURIUM==
-
|PDB= 1dzt |SIZE=350|CAPTION= <scene name='initialview01'>1dzt</scene>, resolution 2.2&Aring;
+
<StructureSection load='1dzt' size='340' side='right'caption='[[1dzt]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TPE:3'-O-ACETYLTHYMIDINE-(5'+DIPHOSPHATE+PHENYL+ESTER)'>TPE</scene>, <scene name='pdbligand=ATY:3'-O-ACETYLTHYMIDINE-5'-DIPHOSPHATE'>ATY</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
+
<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>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_3,5-epimerase dTDP-4-dehydrorhamnose 3,5-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.13 5.1.3.13]
+
</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>
-
|GENE=
+
<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='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>
-
'''RMLC FROM SALMONELLA TYPHIMURIUM'''
+
== 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>
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dz/1dzt_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1dzt ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
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.
-
==About this Structure==
+
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<ref>PMID:10802738</ref>
-
1DZT 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=1DZT OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/10802738 10802738]
+
</div>
-
[[Category: Salmonella typhimurium]]
+
<div class="pdbe-citations 1dzt" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: dTDP-4-dehydrorhamnose 3,5-epimerase]]
+
-
[[Category: Giraud, M F.]]
+
-
[[Category: Naismith, J H.]]
+
-
[[Category: ATY]]
+
-
[[Category: GOL]]
+
-
[[Category: SO4]]
+
-
[[Category: TPE]]
+
-
[[Category: 3]]
+
-
[[Category: 5 hexulose epimerase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:47:13 2008''
+
==See Also==
 +
*[[RmlC|RmlC]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
 +
[[Category: Giraud MF]]
 +
[[Category: Naismith JH]]

Current revision

RMLC FROM SALMONELLA TYPHIMURIUM

PDB ID 1dzt

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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