1xld: Difference between revisions

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[[Image:1xld.jpg|left|200px]]


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==MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT==
The line below this paragraph, containing "STRUCTURE_1xld", creates the "Structure Box" on the page.
<StructureSection load='1xld' size='340' side='right'caption='[[1xld]], [[Resolution|resolution]] 2.50&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'>[[1xld]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_sp._NRRL_B3728 Arthrobacter sp. NRRL B3728]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XLD 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]] 2.5&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</scene></td></tr>
{{STRUCTURE_1xld| PDB=1xld |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xld OCA], [https://pdbe.org/1xld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xld RCSB], [https://www.ebi.ac.uk/pdbsum/1xld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xld ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/XYLA_ARTS7 XYLA_ARTS7]
== 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/xl/1xld_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=1xld ConSurf].
<div style="clear:both"></div>


'''MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT'''
==See Also==
 
*[[D-xylose isomerase|D-xylose isomerase]]
 
*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
==Overview==
__TOC__
The active site and mechanism of D-xylose isomerase have been probed by determination of the crystal structures of the enzyme bound to various substrates, inhibitors and cations. Ring-opening is an obligatory first step of the reaction and is believed to be the rate-determining step for the aldose to ketose conversion. The structure of a complex with a cyclic thio-glucose has been determined and it is concluded that this is an analogue of the Michaelis complex. At -10 degrees C substrates in crystals are observed in the extended chain form. The absence of an appropriately situated base for either the cyclic or extended chain forms from the substrate binding site indicates that the isomerisation does not take place by an enediol or enediolate mechanism. Binding of a trivalent cation places an additional charge at the active site, producing a substrate complex that is analogous to a possible transition state. Of the two binding sites for divalent cations, [1] is permanently occupied under catalytic conditions and is co-ordinated to four carboxylate groups. In the absence of substrate it is exposed to solvent, and in the Michaelis complex analogue, site [1] is octahedrally coordinated, with ligands to O-3 and O-4 of the thiopyranose. In the complex with an open-chain substrate it remains octahedrally co-ordinated, with ligands to O-2 and O-4. Binding at a second cation site [2] is also necessary for catalysis and this site is believed to bind Co2+ more strongly than site [1]. This site is octahedrally co-ordinated to three carboxylate groups (bidentate co-ordination to one of them), an imidazole and a solvent molecule. It is proposed that during the hydride shift the C-O-1 and C-O-2 bonds of the substrate are polarized by the close approach of the site [2] cation. In the transition-state analogue this cation is observed at a site [2'], 1.0 A from site [2] and about 2.7 A from O-1 and O-2 of the substrate. It is likely that co-ordination of the cation to O-1 and O-2 would be concomitant with ionisation of the sugar hydroxyl group. The polarisation of C-O-1 and C-O-2 is assisted by the co-ordination of O-2 to cation [1] and O-1 to a lysine side-chain.(ABSTRACT TRUNCATED AT 400 WORDS)
</StructureSection>
 
[[Category: Arthrobacter sp. NRRL B3728]]
==About this Structure==
[[Category: Large Structures]]
1XLD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XLD OCA].
[[Category: Blow DM]]
 
[[Category: Collyer CA]]
==Reference==
[[Category: Henrick K]]
Mechanism for aldose-ketose interconversion by D-xylose isomerase involving ring opening followed by a 1,2-hydride shift., Collyer CA, Henrick K, Blow DM, J Mol Biol. 1990 Mar 5;212(1):211-35. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2319597 2319597]
[[Category: Arthrobacter sp.]]
[[Category: Single protein]]
[[Category: Xylose isomerase]]
[[Category: Blow, D M.]]
[[Category: Collyer, C A.]]
[[Category: Henrick, K.]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 15:10:59 2008''

Latest revision as of 11:51, 14 February 2024

MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFTMECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT

Structural highlights

1xld is a 2 chain structure with sequence from Arthrobacter sp. NRRL B3728. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYLA_ARTS7

Evolutionary Conservation

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

See Also

1xld, resolution 2.50Å

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