3ext: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,327,076 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,327,076 edits
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:3ext.png|left|200px]]


<!--
==Crystal structure of KGPDC from Streptococcus mutans==
The line below this paragraph, containing "STRUCTURE_3ext", creates the "Structure Box" on the page.
<StructureSection load='3ext' size='340' side='right'caption='[[3ext]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3ext]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EXT FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
{{STRUCTURE_3ext|  PDB=3ext  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ext FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ext OCA], [https://pdbe.org/3ext PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ext RCSB], [https://www.ebi.ac.uk/pdbsum/3ext PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ext ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q93DA8_STRMG Q93DA8_STRMG]
== 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/ex/3ext_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=3ext ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The 3-keto-L-gulonate 6-phosphate decarboxylase (KGPDC) catalyses the decarboxylation of 3-keto-L-gulonate 6-phosphate to L-xylulose in the presence of magnesium ions. The enzyme is involved in L-ascorbate metabolism and plays an essential role in the pathway of glucuronate interconversion. Crystal structures of Streptococcus mutans KGPDC were determined in the absence and presence of the product analog D-ribulose 5-phosphate. We have observed an 8 A alphaB-helix movement and other structural rearrangements around the active site between the apo-structures and product analog bound structure. These drastic conformational changes upon ligand binding are the first observation of this kind for the KGPDC family. The flexibilities of both the alpha-helix lid and the side chains of Arg144 and Arg197 are associated with substrate binding and product releasing. The open-closed conformational changes of the active site, through the movements of the alpha-helix lid and the arginine residues are important for substrate binding and catalysis.


===Crystal structure of KGPDC from Streptococcus mutans===
Open-closed conformational change revealed by the crystal structures of 3-keto-L-gulonate 6-phosphate decarboxylase from Streptococcus mutans.,Li GL, Liu X, Nan J, Brostromer E, Li LF, Su XD Biochem Biophys Res Commun. 2009 Apr 10;381(3):429-33. Epub 2009 Feb 15. PMID:19222992<ref>PMID:19222992</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
3EXT is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EXT OCA].
<div class="pdbe-citations 3ext" style="background-color:#fffaf0;"></div>
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:19222992</ref><references group="xtra"/>
__TOC__
[[Category: 3-dehydro-L-gulonate-6-phosphate decarboxylase]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Streptococcus mutans]]
[[Category: Streptococcus mutans]]
[[Category: Li, G L.]]
[[Category: Li GL]]
[[Category: Li, L F.]]
[[Category: Li LF]]
[[Category: Liu, X.]]
[[Category: Liu X]]
[[Category: Su, X D.]]
[[Category: Su XD]]
[[Category: Beta barrel]]
[[Category: Lyase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 16:48:15 2009''

Latest revision as of 15:24, 1 November 2023

Crystal structure of KGPDC from Streptococcus mutans

3ext, resolution 2.00Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=3ext&oldid=3932962"