1p1x
From Proteopedia
(New page: 200px<br /><applet load="1p1x" size="450" color="white" frame="true" align="right" spinBox="true" caption="1p1x, resolution 0.99Å" /> '''COMPARISON OF CLASS ...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1p1x.gif|left|200px]]<br /><applet load="1p1x" size=" | + | [[Image:1p1x.gif|left|200px]]<br /><applet load="1p1x" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1p1x, resolution 0.99Å" /> | caption="1p1x, resolution 0.99Å" /> | ||
'''COMPARISON OF CLASS I ALDOLASE BINDING SITE ARCHITECTURE BASED ON THE CRYSTAL STRUCTURE OF 2-DEOXYRIBOSE-5-PHOSPHATE ALDOLASE DETERMINED AT 0.99 ANGSTROM RESOLUTION'''<br /> | '''COMPARISON OF CLASS I ALDOLASE BINDING SITE ARCHITECTURE BASED ON THE CRYSTAL STRUCTURE OF 2-DEOXYRIBOSE-5-PHOSPHATE ALDOLASE DETERMINED AT 0.99 ANGSTROM RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of the bacterial (Escherichia coli) class I | + | The crystal structure of the bacterial (Escherichia coli) class I 2-deoxyribose-5-phosphate aldolase (DERA) has been determined by Se-Met multiple anomalous dispersion (MAD) methods at 0.99A resolution. This structure represents the highest-resolution X-ray structure of an aldolase determined to date and enables a true atomic view of the enzyme. The crystal structure shows the ubiquitous TIM alpha/beta barrel fold. The enzyme contains two lysine residues in the active site. Lys167 forms the Schiff base intermediate, whereas Lys201, which is in close vicinity to the reactive lysine residue, is responsible for the perturbed pK(a) of Lys167 and, hence, also a key residue in the reaction mechanism. DERA is the only known aldolase that is able to use aldehydes as both aldol donor and acceptor molecules in the aldol reaction and is, therefore, of particular interest as a biocatalyst in synthetic organic chemistry. The uncomplexed DERA structure enables a detailed comparison with the substrate complexes and highlights a conformational change in the phosphate-binding site. Knowledge of the enzyme active-site environment has been the basis for exploration of catalysis of non-natural substrates and of mutagenesis of the phosphate-binding site to expand substrate specificity. Detailed comparison with other class I aldolase enzymes and DERA enzymes from different organisms reveals a similar geometric arrangement of key residues and implies a potential role for water as a general base in the catalytic mechanism. |
==About this Structure== | ==About this Structure== | ||
| - | 1P1X is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] Full crystallographic information is available from [http:// | + | 1P1X is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P1X OCA]. |
==Reference== | ==Reference== | ||
| Line 15: | Line 15: | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Heine, A.]] | [[Category: Heine, A.]] | ||
| - | [[Category: Luz, J | + | [[Category: Luz, J G.]] |
| - | [[Category: Wilson, I | + | [[Category: Wilson, I A.]] |
| - | [[Category: Wong, C | + | [[Category: Wong, C H.]] |
[[Category: alpha-beta barrel]] | [[Category: alpha-beta barrel]] | ||
[[Category: tim barrel]] | [[Category: tim barrel]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:24:11 2008'' |
Revision as of 12:24, 21 February 2008
|
COMPARISON OF CLASS I ALDOLASE BINDING SITE ARCHITECTURE BASED ON THE CRYSTAL STRUCTURE OF 2-DEOXYRIBOSE-5-PHOSPHATE ALDOLASE DETERMINED AT 0.99 ANGSTROM RESOLUTION
Overview
The crystal structure of the bacterial (Escherichia coli) class I 2-deoxyribose-5-phosphate aldolase (DERA) has been determined by Se-Met multiple anomalous dispersion (MAD) methods at 0.99A resolution. This structure represents the highest-resolution X-ray structure of an aldolase determined to date and enables a true atomic view of the enzyme. The crystal structure shows the ubiquitous TIM alpha/beta barrel fold. The enzyme contains two lysine residues in the active site. Lys167 forms the Schiff base intermediate, whereas Lys201, which is in close vicinity to the reactive lysine residue, is responsible for the perturbed pK(a) of Lys167 and, hence, also a key residue in the reaction mechanism. DERA is the only known aldolase that is able to use aldehydes as both aldol donor and acceptor molecules in the aldol reaction and is, therefore, of particular interest as a biocatalyst in synthetic organic chemistry. The uncomplexed DERA structure enables a detailed comparison with the substrate complexes and highlights a conformational change in the phosphate-binding site. Knowledge of the enzyme active-site environment has been the basis for exploration of catalysis of non-natural substrates and of mutagenesis of the phosphate-binding site to expand substrate specificity. Detailed comparison with other class I aldolase enzymes and DERA enzymes from different organisms reveals a similar geometric arrangement of key residues and implies a potential role for water as a general base in the catalytic mechanism.
About this Structure
1P1X is a Single protein structure of sequence from Escherichia coli. Active as Deoxyribose-phosphate aldolase, with EC number 4.1.2.4 Full crystallographic information is available from OCA.
Reference
Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution., Heine A, Luz JG, Wong CH, Wilson IA, J Mol Biol. 2004 Oct 29;343(4):1019-34. PMID:15476818
Page seeded by OCA on Thu Feb 21 14:24:11 2008
