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1xya
From Proteopedia
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| - | [[Image:1xya.gif|left|200px]] | + | [[Image:1xya.gif|left|200px]] |
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| - | '''X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS''' | + | {{Structure |
| + | |PDB= 1xya |SIZE=350|CAPTION= <scene name='initialview01'>1xya</scene>, resolution 1.81Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=OH:HYDROXIDE ION'>OH</scene> | ||
| + | |ACTIVITY= [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] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1XYA is a [ | + | 1XYA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. This structure supersedes the now removed PDB entry 3XIA. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYA OCA]. |
==Reference== | ==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:// | + | 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: Single protein]] | ||
[[Category: Streptomyces olivochromogenes]] | [[Category: Streptomyces olivochromogenes]] | ||
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[[Category: isomerase(intramolecular oxidoreductase)]] | [[Category: isomerase(intramolecular oxidoreductase)]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:16:05 2008'' |
Revision as of 13:16, 20 March 2008
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| , resolution 1.81Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Activity: | Xylose isomerase, with EC number 5.3.1.5 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS
Overview
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.
About this Structure
1XYA is a Single protein structure of sequence from Streptomyces olivochromogenes. This structure supersedes the now removed PDB entry 3XIA. Full crystallographic information is available from 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:8180169
Page seeded by OCA on Thu Mar 20 15:16:05 2008
