1xis
From Proteopedia
(New page: 200px<br /><applet load="1xis" size="450" color="white" frame="true" align="right" spinBox="true" caption="1xis, resolution 1.60Å" /> '''A METAL-MEDIATED HYD...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1xis.jpg|left|200px]]<br /><applet load="1xis" size=" | + | [[Image:1xis.jpg|left|200px]]<br /><applet load="1xis" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1xis, resolution 1.60Å" /> | caption="1xis, resolution 1.60Å" /> | ||
'''A METAL-MEDIATED HYDRIDE SHIFT MECHANISM FOR XYLOSE ISOMERASE BASED ON THE 1.6 ANGSTROMS STREPTOMYCES RUBIGINOSUS STRUCTURES WITH XYLITOL AND D-XYLOSE'''<br /> | '''A METAL-MEDIATED HYDRIDE SHIFT MECHANISM FOR XYLOSE ISOMERASE BASED ON THE 1.6 ANGSTROMS STREPTOMYCES RUBIGINOSUS STRUCTURES WITH XYLITOL AND D-XYLOSE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of recombinant Streptomyces rubiginosus D-xylose | + | The crystal structure of recombinant Streptomyces rubiginosus D-xylose isomerase (D-xylose keto-isomerase, EC 5.3.1.5) solved by the multiple isomorphous replacement technique has been refined to R = 0.16 at 1.64 A resolution. As observed in an earlier study at 4.0 A (Carrell et al., J. Biol. Chem. 259: 3230-3236, 1984), xylose isomerase is a tetramer composed of four identical subunits. The monomer consists of an eight-stranded parallel beta-barrel surrounded by eight helices with an extended C-terminal tail that provides extensive contacts with a neighboring monomer. The active site pocket is defined by an opening in the barrel whose entrance is lined with hydrophobic residues while the bottom of the pocket consists mainly of glutamate, aspartate, and histidine residues coordinated to two manganese ions. The structures of the enzyme in the presence of MnCl2, the inhibitor xylitol, and the substrate D-xylose in the presence and absence of MnCl2 have also been refined to R = 0.14 at 1.60 A, R = 0.15 at 1.71 A, R = 0.15 at 1.60 A, and R = 0.14 at 1.60 A, respectively. Both the ring oxygen of the cyclic alpha-D-xylose and its C1 hydroxyl are within hydrogen bonding distance of NE2 of His-54 in the structure crystallized in the presence of D-xylose. Both the inhibitor, xylitol, and the extended form of the substrate, D-xylose, bind such that the C2 and C4 OH groups interact with one of the two divalent cations found in the active site and the C1 OH with the other cation. The remainder of the OH groups hydrogen bond with neighboring amino acid side chains. A detailed mechanism for D-xylose isomerase is proposed. Upon binding of cyclic alpha-D-xylose to xylose isomerase, His-54 acts as the catalytic base in a ring opening reaction. The ring opening step is followed by binding of D-xylose, involving two divalent cations, in an extended conformation. The isomerization of D-xylose to D-xylulose involves a metal-mediated 1,2-hydride shift. The final step in the mechanism is a ring closure to produce alpha-D-xylulose. The ring closing is the reverse of the ring opening step. This mechanism accounts for the majority of xylose isomerase's biochemical properties, including (1) the lack of solvent exchange between the 2-position of D-xylose and the 1-pro-R position of D-xylulose, (2) the chemical modification of histidine and lysine, (3) the pH vs. activity profile, and (4) the requirement for two divalent cations in the mechanism. |
==About this Structure== | ==About this Structure== | ||
| - | 1XIS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. 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] Full crystallographic information is available from [http:// | + | 1XIS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus] with <scene name='pdbligand=MN:'>MN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XIS OCA]. |
==Reference== | ==Reference== | ||
| Line 14: | Line 14: | ||
[[Category: Streptomyces rubiginosus]] | [[Category: Streptomyces rubiginosus]] | ||
[[Category: Xylose isomerase]] | [[Category: Xylose isomerase]] | ||
| - | [[Category: Howard, A | + | [[Category: Howard, A J.]] |
[[Category: Whitlow, M.]] | [[Category: Whitlow, M.]] | ||
[[Category: MN]] | [[Category: MN]] | ||
[[Category: isomerase(intramolecular oxidoreductse)]] | [[Category: isomerase(intramolecular oxidoreductse)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:55:12 2008'' |
Revision as of 13:55, 21 February 2008
|
A METAL-MEDIATED HYDRIDE SHIFT MECHANISM FOR XYLOSE ISOMERASE BASED ON THE 1.6 ANGSTROMS STREPTOMYCES RUBIGINOSUS STRUCTURES WITH XYLITOL AND D-XYLOSE
Overview
The crystal structure of recombinant Streptomyces rubiginosus D-xylose isomerase (D-xylose keto-isomerase, EC 5.3.1.5) solved by the multiple isomorphous replacement technique has been refined to R = 0.16 at 1.64 A resolution. As observed in an earlier study at 4.0 A (Carrell et al., J. Biol. Chem. 259: 3230-3236, 1984), xylose isomerase is a tetramer composed of four identical subunits. The monomer consists of an eight-stranded parallel beta-barrel surrounded by eight helices with an extended C-terminal tail that provides extensive contacts with a neighboring monomer. The active site pocket is defined by an opening in the barrel whose entrance is lined with hydrophobic residues while the bottom of the pocket consists mainly of glutamate, aspartate, and histidine residues coordinated to two manganese ions. The structures of the enzyme in the presence of MnCl2, the inhibitor xylitol, and the substrate D-xylose in the presence and absence of MnCl2 have also been refined to R = 0.14 at 1.60 A, R = 0.15 at 1.71 A, R = 0.15 at 1.60 A, and R = 0.14 at 1.60 A, respectively. Both the ring oxygen of the cyclic alpha-D-xylose and its C1 hydroxyl are within hydrogen bonding distance of NE2 of His-54 in the structure crystallized in the presence of D-xylose. Both the inhibitor, xylitol, and the extended form of the substrate, D-xylose, bind such that the C2 and C4 OH groups interact with one of the two divalent cations found in the active site and the C1 OH with the other cation. The remainder of the OH groups hydrogen bond with neighboring amino acid side chains. A detailed mechanism for D-xylose isomerase is proposed. Upon binding of cyclic alpha-D-xylose to xylose isomerase, His-54 acts as the catalytic base in a ring opening reaction. The ring opening step is followed by binding of D-xylose, involving two divalent cations, in an extended conformation. The isomerization of D-xylose to D-xylulose involves a metal-mediated 1,2-hydride shift. The final step in the mechanism is a ring closure to produce alpha-D-xylulose. The ring closing is the reverse of the ring opening step. This mechanism accounts for the majority of xylose isomerase's biochemical properties, including (1) the lack of solvent exchange between the 2-position of D-xylose and the 1-pro-R position of D-xylulose, (2) the chemical modification of histidine and lysine, (3) the pH vs. activity profile, and (4) the requirement for two divalent cations in the mechanism.
About this Structure
1XIS is a Single protein structure of sequence from Streptomyces rubiginosus with as ligand. Active as Xylose isomerase, with EC number 5.3.1.5 Full crystallographic information is available from OCA.
Reference
A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose., Whitlow M, Howard AJ, Finzel BC, Poulos TL, Winborne E, Gilliland GL, Proteins. 1991;9(3):153-73. PMID:2006134
Page seeded by OCA on Thu Feb 21 15:55:12 2008
