1ede

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:01, 7 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ede.gif|left|200px]]
 
-
<!--
+
==REFINED X-RAY STRUCTURES OF HALOALKANE DEHALOGENASE AT PH 6.2 AND PH 8.2 AND IMPLICATIONS FOR THE REACTION MECHANISM==
-
The line below this paragraph, containing "STRUCTURE_1ede", creates the "Structure Box" on the page.
+
<StructureSection load='1ede' size='340' side='right'caption='[[1ede]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1ede]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthobacter_autotrophicus Xanthobacter autotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EDE FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</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=1ede FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ede OCA], [https://pdbe.org/1ede PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ede RCSB], [https://www.ebi.ac.uk/pdbsum/1ede PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ede ProSAT]</span></td></tr>
-
{{STRUCTURE_1ede| PDB=1ede | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DHLA_XANAU DHLA_XANAU] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Has a broad substrate specificity, which includes terminally mono- and di- chlorinated and brominated alkanes (up to C4 only). The highest activity was found with 1,2-dichloroethane, 1,3-dichloropropane, and 1,2-dibromoethane.
 +
== 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/ed/1ede_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ede ConSurf].
 +
<div style="clear:both"></div>
-
'''REFINED X-RAY STRUCTURES OF HALOALKANE DEHALOGENASE AT PH 6.2 AND PH 8.2 AND IMPLICATIONS FOR THE REACTION MECHANISM'''
+
==See Also==
-
 
+
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The crystal structure of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 has been refined at 1.9 A resolution at two different pH values, the pH of crystallization (pH 6.2) and the pH of optimal activity (pH 8.2), to final R-factors of 16.8% and 16.4%, respectively. Both models show good stereochemical quality. Two non-glycine residues have main-chain torsion angles that are located outside the "allowed" regions in a Ramachandran plot. One of them is the nucleophilic residue Asp124, which, together with the two other active site residues His289 and Asp260, is situated in an internal, predominantly hydrophobic cavity. The other residue, Asn148, helps stabilize the conformations of two of these active-site residues, Asp124 and Asp260. Comparison of the models at pH 6.2 and pH 8.2 revealed one major structural difference. At pH 6.2, a salt-bridge is present between the N epsilon 2 atom of His289 and the O delta 1 atom of Asp124, while at pH 8.2, this salt-bridge is absent, indicating that the N epsilon 2 atom of the histidine residue is mostly deprotonated at the pH of optimum activity. This is in agreement with the putative reaction mechanism in which the O delta 1 atom of Asp124 performs a nucleophilic attack on the substrate, resulting in an intermediate ester. This ester is subsequently cleaved by a hydrolytic water molecule. The high-resolution data sets clearly show the exact position of this water molecule. It is in an ideal position for donating a proton to the N epsilon 2 atom of His289 and subsequently cleaving the covalently bound intermediate ester, releasing the alcohol product. Detailed investigation of both refined models showed a number of unusual structural features. Four out of 11 helices contain an internal proline residue other than in the first turn. Two other alpha-helices have adopted in their central part a 3(10) conformation. A novel four-residue turn between a helix and a strand, the alpha beta 4 turn, is located at the site of the bend in the central eight-stranded beta-sheet of the dehalogenase structure.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1EDE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Xanthobacter_autotrophicus Xanthobacter autotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EDE OCA].
+
-
 
+
-
==Reference==
+
-
Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism., Verschueren KH, Franken SM, Rozeboom HJ, Kalk KH, Dijkstra BW, J Mol Biol. 1993 Aug 5;232(3):856-72. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8355275 8355275]
+
-
[[Category: Haloalkane dehalogenase]]
+
-
[[Category: Single protein]]
+
[[Category: Xanthobacter autotrophicus]]
[[Category: Xanthobacter autotrophicus]]
-
[[Category: Dijkstra, B W.]]
+
[[Category: Dijkstra BW]]
-
[[Category: Verschueren, K H.G.]]
+
[[Category: Verschueren KHG]]
-
[[Category: Dehalogenase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 14:57:39 2008''
+

Current revision

REFINED X-RAY STRUCTURES OF HALOALKANE DEHALOGENASE AT PH 6.2 AND PH 8.2 AND IMPLICATIONS FOR THE REACTION MECHANISM

PDB ID 1ede

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ede"
Personal tools