2gve
From Proteopedia
(New page: 200px<br /><applet load="2gve" size="450" color="white" frame="true" align="right" spinBox="true" caption="2gve, resolution 2.2Å" /> '''Time-of-Flight Neutro...) |
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| - | [[Image:2gve.gif|left|200px]]<br /><applet load="2gve" size=" | + | [[Image:2gve.gif|left|200px]]<br /><applet load="2gve" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2gve, resolution 2.2Å" /> | caption="2gve, resolution 2.2Å" /> | ||
'''Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase'''<br /> | '''Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Time-of-flight neutron diffraction has been used to locate hydrogen atoms | + | Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at high resolution (1.8 A) by this method. We have determined the position and orientation of a metal ion-bound water molecule that is located in the active site of the enzyme; this water has been thought to be involved in the isomerization step in which D-xylose is converted to D-xylulose or D-glucose to D-fructose. It is shown to be water (rather than a hydroxyl group) under the conditions of measurement (pH 8.0). Our analyses also reveal that one lysine probably has an -NH(2)-terminal group (rather than NH(3)(+)). The ionization state of each histidine residue also was determined. High-resolution x-ray studies (at 0.94 A) indicate disorder in some side chains when a truncated substrate is bound and suggest how some side chains might move during catalysis. This combination of time-of-flight neutron diffraction and x-ray diffraction can contribute greatly to the elucidation of enzyme mechanisms. |
==About this Structure== | ==About this Structure== | ||
| - | 2GVE 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 CO and DOD 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] Full crystallographic information is available from [http:// | + | 2GVE 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=CO:'>CO</scene> and <scene name='pdbligand=DOD:'>DOD</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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GVE OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Streptomyces rubiginosus]] | [[Category: Streptomyces rubiginosus]] | ||
[[Category: Xylose isomerase]] | [[Category: Xylose isomerase]] | ||
| - | [[Category: Bunick, G | + | [[Category: Bunick, G J.]] |
| - | [[Category: Carrell, H | + | [[Category: Carrell, H L.]] |
[[Category: Coates, L.]] | [[Category: Coates, L.]] | ||
| - | [[Category: Glusker, J | + | [[Category: Glusker, J P.]] |
| - | [[Category: Hanson, B | + | [[Category: Hanson, B L.]] |
| - | [[Category: Katz, A | + | [[Category: Katz, A K.]] |
[[Category: Langan, P.]] | [[Category: Langan, P.]] | ||
[[Category: Li, X.]] | [[Category: Li, X.]] | ||
| - | [[Category: Schoenborn, B | + | [[Category: Schoenborn, B P.]] |
[[Category: CO]] | [[Category: CO]] | ||
[[Category: DOD]] | [[Category: DOD]] | ||
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[[Category: two metal binding sites]] | [[Category: two metal binding sites]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:35:49 2008'' |
Revision as of 15:35, 21 February 2008
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Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase
Overview
Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at high resolution (1.8 A) by this method. We have determined the position and orientation of a metal ion-bound water molecule that is located in the active site of the enzyme; this water has been thought to be involved in the isomerization step in which D-xylose is converted to D-xylulose or D-glucose to D-fructose. It is shown to be water (rather than a hydroxyl group) under the conditions of measurement (pH 8.0). Our analyses also reveal that one lysine probably has an -NH(2)-terminal group (rather than NH(3)(+)). The ionization state of each histidine residue also was determined. High-resolution x-ray studies (at 0.94 A) indicate disorder in some side chains when a truncated substrate is bound and suggest how some side chains might move during catalysis. This combination of time-of-flight neutron diffraction and x-ray diffraction can contribute greatly to the elucidation of enzyme mechanisms.
About this Structure
2GVE is a Single protein structure of sequence from Streptomyces rubiginosus with and as ligands. Active as Xylose isomerase, with EC number 5.3.1.5 Full crystallographic information is available from OCA.
Reference
Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction., Katz AK, Li X, Carrell HL, Hanson BL, Langan P, Coates L, Schoenborn BP, Glusker JP, Bunick GJ, Proc Natl Acad Sci U S A. 2006 May 30;103(22):8342-7. Epub 2006 May 17. PMID:16707576
Page seeded by OCA on Thu Feb 21 17:35:49 2008
Categories: Single protein | Streptomyces rubiginosus | Xylose isomerase | Bunick, G J. | Carrell, H L. | Coates, L. | Glusker, J P. | Hanson, B L. | Katz, A K. | Langan, P. | Li, X. | Schoenborn, B P. | CO | DOD | Protonation states of residues | Tim barrel-beta-alpha-barrels | Two metal binding sites
