2no4

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure analysis of a Dehalogenase

Structural highlights

2no4 is a 2 chain structure with sequence from Burkholderia cepacia. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.93Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HAD4_BURCE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Schmidberger JW, Wilce JA, Tsang JS, Wilce MC. Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4. J Mol Biol. 2007 May 4;368(3):706-17. Epub 2007 Feb 20. PMID:17368477 doi:10.1016/j.jmb.2007.02.015

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2no4"

Categories: Burkholderia cepacia | Large Structures | Schmidberger JW | Wilce MCJ

@@ Line 1: / Line 1: @@
 ==Crystal Structure analysis of a Dehalogenase==
-<StructureSection load='2no4' size='340' side='right' caption='[[2no4]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
+<StructureSection load='2no4' size='340' side='right'caption='[[2no4]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2no4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_cepacia"_burkholder_1950 "pseudomonas cepacia" burkholder 1950]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NO4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NO4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2no4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NO4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NO4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2no5|2no5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrolase Hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.2 3.8.1.2] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2no4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2no4 OCA], [https://pdbe.org/2no4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2no4 RCSB], [https://www.ebi.ac.uk/pdbsum/2no4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2no4 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/2no4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2no4 RCSB], [http://www.ebi.ac.uk/pdbsum/2no4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2no4 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/HAD4_BURCE HAD4_BURCE]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/no/2no4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/no/2no4_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 2no4" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Pseudomonas cepacia burkholder 1950]]
+[[Category: Burkholderia cepacia]]
-[[Category: Hydrolase]]
+[[Category: Large Structures]]
-[[Category: Schmidberger, J W]]
+[[Category: Schmidberger JW]]
-[[Category: Wilce, M C.J]]
+[[Category: Wilce MCJ]]
-[[Category: Had superfamily]]
-[[Category: Haloacid dehalogenase]]
-[[Category: Rossmann fold]]

2no4

From Proteopedia

Current revision

Crystal Structure analysis of a Dehalogenase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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