1zo8

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:11, 23 August 2023) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1zo8.gif|left|200px]]<br /><applet load="1zo8" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1zo8, resolution 1.90&Aring;" />
 
-
'''X-ray Structure of the haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in complex with (S)-para-nitrostyrene oxide, with a water molecule in the halide-binding site'''<br />
 
-
==Overview==
+
==X-ray Structure of the haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in complex with (S)-para-nitrostyrene oxide, with a water molecule in the halide-binding site==
 +
<StructureSection load='1zo8' size='340' side='right'caption='[[1zo8]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1zo8]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZO8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZO8 FirstGlance]. <br>
 +
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SNO:(S)-PARA-NITROSTYRENE+OXIDE'>SNO</scene></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=1zo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zo8 OCA], [https://pdbe.org/1zo8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zo8 RCSB], [https://www.ebi.ac.uk/pdbsum/1zo8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zo8 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q93D82_RHIRD Q93D82_RHIRD]
 +
== 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/zo/1zo8_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=1zo8 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
Halo alcohol dehalogenase HheC catalyzes the highly enantioselective dehalogenation of vicinal halo alcohols to epoxides, as well as the reverse reaction, the enantioselective and beta-regioselective nucleophilic ring opening of epoxides by pseudo-halides such as azide and cyanide. To investigate this latter reaction, we determined X-ray structures of complexes of HheC with the favored and unfavored enantiomers of para-nitrostyrene oxide. The aromatic parts of the two enantiomers bind in a very similar way, but the epoxide ring of the unfavored (S)-enantiomer binds in a nonproductive inverted manner, with the epoxide oxygen and Cbeta atom positions interchanged with respect to those of the favored (R)-enantiomer. The calculated difference in relative Gibbs binding energy is in agreement with the observed loss of a single hydrogen bond in the S bound state with respect to the R bound state. Our results indicate that it is the nonproductive binding of the unfavored (S)-enantiomer, rather than the difference in affinity for the two enantiomers, that allows HheC to catalyze the azide-mediated ring opening of para-nitrostyrene oxide with high enantioselectivity. This work represents a rare opportunity to explain the enantioselectivity of an enzymatic reaction by comparison of crystallographic data on the binding of both the favored and unfavored enantiomers.
Halo alcohol dehalogenase HheC catalyzes the highly enantioselective dehalogenation of vicinal halo alcohols to epoxides, as well as the reverse reaction, the enantioselective and beta-regioselective nucleophilic ring opening of epoxides by pseudo-halides such as azide and cyanide. To investigate this latter reaction, we determined X-ray structures of complexes of HheC with the favored and unfavored enantiomers of para-nitrostyrene oxide. The aromatic parts of the two enantiomers bind in a very similar way, but the epoxide ring of the unfavored (S)-enantiomer binds in a nonproductive inverted manner, with the epoxide oxygen and Cbeta atom positions interchanged with respect to those of the favored (R)-enantiomer. The calculated difference in relative Gibbs binding energy is in agreement with the observed loss of a single hydrogen bond in the S bound state with respect to the R bound state. Our results indicate that it is the nonproductive binding of the unfavored (S)-enantiomer, rather than the difference in affinity for the two enantiomers, that allows HheC to catalyze the azide-mediated ring opening of para-nitrostyrene oxide with high enantioselectivity. This work represents a rare opportunity to explain the enantioselectivity of an enzymatic reaction by comparison of crystallographic data on the binding of both the favored and unfavored enantiomers.
-
==About this Structure==
+
Structural basis for the enantioselectivity of an epoxide ring opening reaction catalyzed by halo alcohol dehalogenase HheC.,de Jong RM, Tiesinga JJ, Villa A, Tang L, Janssen DB, Dijkstra BW J Am Chem Soc. 2005 Sep 28;127(38):13338-43. PMID:16173767<ref>PMID:16173767</ref>
-
1ZO8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens] with <scene name='pdbligand=SNO:'>SNO</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZO8 OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structural basis for the enantioselectivity of an epoxide ring opening reaction catalyzed by halo alcohol dehalogenase HheC., de Jong RM, Tiesinga JJ, Villa A, Tang L, Janssen DB, Dijkstra BW, J Am Chem Soc. 2005 Sep 28;127(38):13338-43. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16173767 16173767]
+
</div>
-
[[Category: Agrobacterium tumefaciens]]
+
<div class="pdbe-citations 1zo8" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: Dijkstra, B W.]]
+
-
[[Category: Janssen, D B.]]
+
-
[[Category: Jong, R M.de.]]
+
-
[[Category: Tang, L.]]
+
-
[[Category: Tiesinga, J J.W.]]
+
-
[[Category: Villa, A.]]
+
-
[[Category: SNO]]
+
-
[[Category: enantioselectivity]]
+
-
[[Category: haloalcohol dehalogenase]]
+
-
[[Category: halohydrin dehalogenase]]
+
-
[[Category: short-chain dehydrogenase/reductase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:17:29 2008''
+
==See Also==
 +
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Agrobacterium tumefaciens]]
 +
[[Category: Large Structures]]
 +
[[Category: Dijkstra BW]]
 +
[[Category: Janssen DB]]
 +
[[Category: Tang L]]
 +
[[Category: Tiesinga JJW]]
 +
[[Category: Villa A]]
 +
[[Category: De Jong RM]]

Current revision

X-ray Structure of the haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in complex with (S)-para-nitrostyrene oxide, with a water molecule in the halide-binding site

PDB ID 1zo8

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools