1epz: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
New page: left|200px<br /><applet load="1epz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1epz, resolution 1.75Å" /> '''CRYSTAL STRUCTURE OF...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(17 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1epz.jpg|left|200px]]<br /><applet load="1epz" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1epz, resolution 1.75&Aring;" />
'''CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOASE 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM WITH BOUND LIGAND.'''<br />


==Overview==
==CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOASE 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM WITH BOUND LIGAND.==
Deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-d-hexulose 3, 5-epimerase, (RmlC) is involved in the biosynthesis of dTDP-l-rhamnose, which is an, essential component of the bacterial cell wall. The crystal structure of, RmlC from Methanobacterium thermoautotrophicum was determined in the, presence and absence of dTDP, a substrate analogue. RmlC is a homodimer, comprising a central jelly roll motif, which extends in two directions, into longer beta-sheets. Binding of dTDP is stabilized by ionic, interactions to the phosphate group and by a combination of ionic and, hydrophobic interactions with the base. The active site, which is located, in the center of the jelly roll, is formed by residues that are conserved, in all known RmlC sequence homologues. The conservation of the active site, residues suggests that the mechanism of action is also conserved and that, the RmlC structure may be useful in guiding the design of antibacterial, drugs.
<StructureSection load='1epz' size='340' side='right'caption='[[1epz]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1epz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EPZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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=1epz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1epz OCA], [https://pdbe.org/1epz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1epz RCSB], [https://www.ebi.ac.uk/pdbsum/1epz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1epz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RMLC_METTH RMLC_METTH] 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:10827167</ref>
== Evolutionary Conservation ==
[[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/ep/1epz_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=1epz ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1EPZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus] with TYD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EPZ OCA].
*[[RmlC|RmlC]]
 
== References ==
==Reference==
<references/>
Crystal structure of dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase from Methanobacterium thermoautotrophicum complexed with dTDP., Christendat D, Saridakis V, Dharamsi A, Bochkarev A, Pai EF, Arrowsmith CH, Edwards AM, J Biol Chem. 2000 Aug 11;275(32):24608-12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10827167 10827167]
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Single protein]]
[[Category: Arrowsmith C]]
[[Category: dTDP-4-dehydrorhamnose 3,5-epimerase]]
[[Category: Bochkarev A]]
[[Category: Arrowsmith, C.]]
[[Category: Christendat D]]
[[Category: Bochkarev, A.]]
[[Category: Edwards AM]]
[[Category: Christendat, D.]]
[[Category: Pai EF]]
[[Category: Edwards, A.M.]]
[[Category: Saridakis V]]
[[Category: Pai, E.F.]]
[[Category: Saridakis, V.]]
[[Category: TYD]]
[[Category: dtdp-4-dehydrorhamnose epimerase]]
[[Category: racemase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:41:14 2007''
Retrieved from "https://proteopedia.org/1epz"