This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1xyb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:53, 14 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1xyb.gif|left|200px]]
 
-
{{Structure
+
==X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS==
-
|PDB= 1xyb |SIZE=350|CAPTION= <scene name='initialview01'>1xyb</scene>, resolution 1.96&Aring;
+
<StructureSection load='1xyb' size='340' side='right'caption='[[1xyb]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
+
<table><tr><td colspan='2'>[[1xyb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XYB FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[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] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xyb OCA], [https://pdbe.org/1xyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xyb RCSB], [https://www.ebi.ac.uk/pdbsum/1xyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xyb ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xyb OCA], [http://www.ebi.ac.uk/pdbsum/1xyb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xyb RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/XYLA_STROL XYLA_STROL] Involved in D-xylose catabolism.
 +
== 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/xy/1xyb_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=1xyb ConSurf].
 +
<div style="clear:both"></div>
-
'''X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS'''
+
==See Also==
-
 
+
*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
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.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1XYB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYB OCA].
+
-
 
+
-
==Reference==
+
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/8180169 8180169]
+
-
[[Category: Single protein]]
+
[[Category: Streptomyces olivochromogenes]]
[[Category: Streptomyces olivochromogenes]]
-
[[Category: Xylose isomerase]]
+
[[Category: Allen KN]]
-
[[Category: Allen, K N.]]
+
[[Category: Lavie A]]
-
[[Category: Lavie, A.]]
+
[[Category: Petsko GA]]
-
[[Category: Petsko, G A.]]
+
[[Category: Ringe D]]
-
[[Category: Ringe, D.]]
+
-
[[Category: isomerase(intramolecular oxidoreductase)]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:56:17 2008''
+

Current revision

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

PDB ID 1xyb

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1xyb"
Personal tools