1qq5: Difference between revisions
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|PDB= 1qq5 |SIZE=350|CAPTION= <scene name='initialview01'>1qq5</scene>, resolution 1.52Å | |PDB= 1qq5 |SIZE=350|CAPTION= <scene name='initialview01'>1qq5</scene>, resolution 1.52Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=FMT:FORMIC ACID'>FMT</scene> | |LIGAND= <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/(S)-2-haloacid_dehalogenase (S)-2-haloacid dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.2 3.8.1.2] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-haloacid_dehalogenase (S)-2-haloacid dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.2 3.8.1.2] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1qq6|1QQ6]], [[1qq7|1QQ7]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qq5 OCA], [http://www.ebi.ac.uk/pdbsum/1qq5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qq5 RCSB]</span> | |||
}} | }} | ||
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[[Category: Ridder, I S.]] | [[Category: Ridder, I S.]] | ||
[[Category: Rozeboom, H J.]] | [[Category: Rozeboom, H J.]] | ||
[[Category: hydrolase]] | [[Category: hydrolase]] | ||
[[Category: l-2-haloacid dehalogenase]] | [[Category: l-2-haloacid dehalogenase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:17:23 2008'' | ||
Revision as of 23:17, 30 March 2008
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| , resolution 1.52Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | (S)-2-haloacid dehalogenase, with EC number 3.8.1.2 | ||||||
| Related: | 1QQ6, 1QQ7
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS
OverviewOverview
The L-2-haloacid dehalogenase from the 1,2-dichloroethane-degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoates to their corresponding D-2-hydroxyalkanoates, with inversion of the configuration at the C(2) atom. The structure of the apoenzyme at pH 8 was refined at 1.5-A resolution. By lowering the pH, the catalytic activity of the enzyme was considerably reduced, allowing the crystal structure determination of the complexes with L-2-monochloropropionate and monochloroacetate at 1.7 and 2.1 A resolution, respectively. Both complexes showed unambiguous electron density extending from the nucleophile Asp(8) to the C(2) atom of the dechlorinated substrates corresponding to a covalent enzyme-ester reaction intermediate. The halide ion that is cleaved off is found in line with the Asp(8) Odelta1-C(2) bond in a halide-stabilizing cradle made up of Arg(39), Asn(115), and Phe(175). In both complexes, the Asp(8) Odelta2 carbonyl oxygen atom interacts with Thr(12), Ser(171), and Asn(173), which possibly constitute the oxyanion hole in the hydrolysis of the ester bond. The carboxyl moiety of the substrate is held in position by interactions with Ser(114), Lys(147), and main chain NH groups. The L-2-monochloropropionate CH(3) group is located in a small pocket formed by side chain atoms of Lys(147), Asn(173), Phe(175), and Asp(176). The size and position of the pocket explain the stereospecificity and the limited substrate specificity of the enzyme. These crystallographic results demonstrate that the reaction of the enzyme proceeds via the formation of a covalent enzyme-ester intermediate at the nucleophile Asp(8).
About this StructureAbout this Structure
1QQ5 is a Single protein structure of sequence from Xanthobacter autotrophicus. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase., Ridder IS, Rozeboom HJ, Kalk KH, Dijkstra BW, J Biol Chem. 1999 Oct 22;274(43):30672-8. PMID:10521454
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