1xya: Difference between revisions

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<StructureSection load='1xya' size='340' side='right'caption='[[1xya]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
<StructureSection load='1xya' size='340' side='right'caption='[[1xya]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1xya]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_olivochromogenus"_(sic)_waksman_1923 "actinomyces olivochromogenus" (sic) waksman 1923]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3xia 3xia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XYA FirstGlance]. <br>
<table><tr><td colspan='2'>[[1xya]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3xia 3xia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XYA FirstGlance]. <br>
</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>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.81&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></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>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=1xya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xya OCA], [https://pdbe.org/1xya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xya RCSB], [https://www.ebi.ac.uk/pdbsum/1xya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xya ProSAT]</span></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=1xya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xya OCA], [https://pdbe.org/1xya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xya RCSB], [https://www.ebi.ac.uk/pdbsum/1xya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xya ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/XYLA_STROL XYLA_STROL]] Involved in D-xylose catabolism.  
[https://www.uniprot.org/uniprot/XYLA_STROL XYLA_STROL] Involved in D-xylose catabolism.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1xya ConSurf].
</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=1xya ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The X-ray crystallographic structures of the metal-activated enzyme xylose isomerase from Streptomyces olivochromogenes with the substrates D-glucose, 3-O-methyl-D-glucose and in the absence of substrate were determined to 1.96-, 2.19-, and 1.81-A resolution and refined to R-factors of 16.6%, 15.9%, and 16.1%, respectively. Xylose isomerase catalyzes the interconversion between glucose and fructose (xylose and xylulose under physiological conditions) by utilizing two metal cofactors to promote a hydride shift; the metals are bridged by a glutamate residue. This puts xylose isomerase in the small but rapidly growing family of enzymes with a bridged bimetallic active site, in which both metals are involved in the chemical transformation. The substrate 3-O-methylglucose was chosen in order to position the glucose molecule in the observed electron density unambiguously. Of the two essential magnesium ions per active site, Mg-2 was observed to occupy two alternate positions, separated by 1.8 A, in the substrate-soaked structures. The deduced movement was not observed in the structure without substrate present and is attributed to a step following substrate binding but prior to isomerization. The substrates glucose and 3-O-methylglucose are observed in their linear extended forms and make identical interactions with the enzyme by forming ligands to Mg-1 through O2 and O4 and by forming hydrogen bonds with His53 through O5 and Lys182 through O1. Mg-2 has a water ligand that is interpreted in the crystal structure in the absence of substrate as a hydroxide ion and in the presence of substrate as a water molecule. This hydroxide ion may act as a base to deprotonate the glucose O2 and subsequently protonate the product fructose O1 concomitant with hydride transfer. Calculations of the solvent-accessible surface of possible dimers, with and without the alpha-helical C-terminal domain, suggest that the tetramer is the active form of this xylose isomerase.
X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis.,Lavie A, Allen KN, Petsko GA, Ringe D Biochemistry. 1994 May 10;33(18):5469-80. PMID:8180169<ref>PMID:8180169</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1xya" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[D-xylose isomerase|D-xylose isomerase]]
*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Xylose isomerase]]
[[Category: Streptomyces olivochromogenes]]
[[Category: Allen, K N]]
[[Category: Allen KN]]
[[Category: Lavie, A]]
[[Category: Lavie A]]
[[Category: Petsko, G A]]
[[Category: Petsko GA]]
[[Category: Ringe, D]]
[[Category: Ringe D]]
[[Category: Isomerase]]
[[Category: Oxidoreductase]]

Latest revision as of 11:53, 14 February 2024

X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSISX-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS

Structural highlights

1xya is a 2 chain structure with sequence from Streptomyces olivochromogenes. This structure supersedes the now removed PDB entry 3xia. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.81Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYLA_STROL Involved in D-xylose catabolism.

Evolutionary Conservation

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

See Also

1xya, resolution 1.81Å

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