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[[Image:1xlm.jpg|left|200px]]<br /><applet load="1xlm" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1xlm, resolution 2.4&Aring;" />
'''D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOL'''<br />


==Overview==
==D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOL==
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 load='1xlm' size='340' side='right'caption='[[1xlm]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1xlm]] 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=1XLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XLM 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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AL:ALUMINUM+ION'>AL</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</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=1xlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xlm OCA], [https://pdbe.org/1xlm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xlm RCSB], [https://www.ebi.ac.uk/pdbsum/1xlm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xlm 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/1xlm_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=1xlm ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structure of the D254.256E double mutant of Arthrobacter xylose isomerase with Al3+ at both metal-binding sites was determined by the molecular replacement method at a conventional R-factor of 0.179. Binding of the two Al3+ does not alter the overall structure significantly. However, there are local rearrangements in the octahedral co-ordination sphere of the Al3+. The inhibitor molecule moves somewhat away from the active site. Furthermore, evidence was revealed for metal ion movement from site 2(1) to site 2(2) upon double mutation. Xylose isomerase requires two divalent metal cations for activation. The catalytic metal ion is translocated 1.8 A away from its initial position during the catalytic reaction. The fact that both activating and inactivating metals (including Al3+) were found exclusively at a single location in the double mutant was an indication that the consequently missing shuttle may account for the crippled catalytic efficiency.


==About this Structure==
Structure determination and refinement of the Al3+ complex of the D254,256E mutant of Arthrobacter D-xylose isomerase at 2.40 A resolution. Further evidence for inhibitor-induced metal ion movement.,Gerczei T, Bocskei Z, Szabo E, Asboth B, Naray-Szabo G Int J Biol Macromol. 1999 Aug;25(4):329-36. PMID:10456773<ref>PMID:10456773</ref>
1XLM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.] with <scene name='pdbligand=XYL:'>XYL</scene> and <scene name='pdbligand=AL:'>AL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] Known structural/functional Sites: <scene name='pdbsite=CTA:Catalytic+Site'>CTA</scene> and <scene name='pdbsite=CTB:Catalytic+Site'>CTB</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XLM OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=2319597 2319597]
</div>
[[Category: Arthrobacter sp.]]
<div class="pdbe-citations 1xlm" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
[[Category: Xylose isomerase]]
[[Category: Asboth, B.]]
[[Category: Bocskei, Z S.]]
[[Category: Gerczei, T.]]
[[Category: Naray-Szabo, G.]]
[[Category: Szabo, E.]]
[[Category: AL]]
[[Category: XYL]]
[[Category: al]]
[[Category: isomerase]]
[[Category: pentose shunt]]
[[Category: substrate induced metal ion movement]]
[[Category: xylose metabolism]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:56:08 2008''
==See Also==
*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arthrobacter sp. NRRL B3728]]
[[Category: Large Structures]]
[[Category: Asboth B]]
[[Category: Bocskei ZS]]
[[Category: Gerczei T]]
[[Category: Naray-Szabo G]]
[[Category: Szabo E]]

Latest revision as of 09:39, 9 August 2023

D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOLD254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOL

Structural highlights

1xlm 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 2.4Å
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.

Publication Abstract from PubMed

The structure of the D254.256E double mutant of Arthrobacter xylose isomerase with Al3+ at both metal-binding sites was determined by the molecular replacement method at a conventional R-factor of 0.179. Binding of the two Al3+ does not alter the overall structure significantly. However, there are local rearrangements in the octahedral co-ordination sphere of the Al3+. The inhibitor molecule moves somewhat away from the active site. Furthermore, evidence was revealed for metal ion movement from site 2(1) to site 2(2) upon double mutation. Xylose isomerase requires two divalent metal cations for activation. The catalytic metal ion is translocated 1.8 A away from its initial position during the catalytic reaction. The fact that both activating and inactivating metals (including Al3+) were found exclusively at a single location in the double mutant was an indication that the consequently missing shuttle may account for the crippled catalytic efficiency.

Structure determination and refinement of the Al3+ complex of the D254,256E mutant of Arthrobacter D-xylose isomerase at 2.40 A resolution. Further evidence for inhibitor-induced metal ion movement.,Gerczei T, Bocskei Z, Szabo E, Asboth B, Naray-Szabo G Int J Biol Macromol. 1999 Aug;25(4):329-36. PMID:10456773[1]

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

See Also

References

  1. ↑ Gerczei T, Bocskei Z, Szabo E, Asboth B, Naray-Szabo G. Structure determination and refinement of the Al3+ complex of the D254,256E mutant of Arthrobacter D-xylose isomerase at 2.40 A resolution. Further evidence for inhibitor-induced metal ion movement. Int J Biol Macromol. 1999 Aug;25(4):329-36. PMID:10456773

1xlm, resolution 2.40Å

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