2no4
From Proteopedia
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|PDB= 2no4 |SIZE=350|CAPTION= <scene name='initialview01'>2no4</scene>, resolution 1.930Å | |PDB= 2no4 |SIZE=350|CAPTION= <scene name='initialview01'>2no4</scene>, resolution 1.930Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=[[2no5|2NO5]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2no4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2no4 OCA], [http://www.ebi.ac.uk/pdbsum/2no4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2no4 RCSB]</span> | ||
}} | }} | ||
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[[Category: Schmidberger, J W.]] | [[Category: Schmidberger, J W.]] | ||
[[Category: Wilce, M C.J.]] | [[Category: Wilce, M C.J.]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: SO4]] | ||
[[Category: had superfamily]] | [[Category: had superfamily]] | ||
[[Category: haloacid dehalogenase]] | [[Category: haloacid dehalogenase]] | ||
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[[Category: rossman fold]] | [[Category: rossman fold]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:05:53 2008'' |
Revision as of 01:05, 31 March 2008
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| , resolution 1.930Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | (S)-2-haloacid dehalogenase, with EC number 3.8.1.2 | ||||||
| Related: | 2NO5
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure analysis of a Dehalogenase
Overview
DehIVa is a haloacid dehalogenase (EC 3.8.1.2) from the soil and water borne bacterium Burkholderia cepacia MBA4, which belongs to the functionally variable haloacid dehalogenase (HAD) superfamily of enzymes. The haloacid dehalogenases catalyse the removal of halides from haloacids resulting in a hydroxlated product. These enzymes are of interest for their potential to degrade recalcitrant halogenated environmental pollutants and their use in the synthesis of industrial chemicals. The haloacid dehalogenases utilise a nucleophilic attack on the substrate by an aspartic acid residue to form an enzyme-substrate ester bond and concomitantly cleaving of the carbon-halide bond and release of a hydroxylated product following ester hydrolysis. We present the crystal structures of both the substrate-free DehIVa refined to 1.93 A resolution and DehIVa covalently bound to l-2-monochloropropanoate trapped as a reaction intermediate, refined to 2.7 A resolution. Electron density consistent with a previously unidentified yet anticipated water molecule in the active site poised to donate its hydroxyl group to the product and its proton to the catalytic Asp11 is evident. It has been unclear how substrate enters the active site of this and related enzymes. The results of normal mode analysis (NMA) are presented and suggest a means whereby the predicted global dynamics of the enzyme allow for entry of the substrate into the active site. In the context of these results, the possible role of Arg42 and Asn178 in a "lock down" mechanism affecting active site access is discussed. In silico substrate docking of enantiomeric substrates has been examined in order to evaluate the enzymes enantioselectivity.
About this Structure
2NO4 is a Single protein structure of sequence from Burkholderia cepacia. Full crystallographic information is available from OCA.
Reference
Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4., Schmidberger JW, Wilce JA, Tsang JS, Wilce MC, J Mol Biol. 2007 May 4;368(3):706-17. Epub 2007 Feb 20. PMID:17368477
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