1bn6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:37, 7 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1bn6.jpg|left|200px]]<br /><applet load="1bn6" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1bn6, resolution 1.5&Aring;" />
 
-
'''HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES'''<br />
 
-
==Overview==
+
==HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES==
-
The hydrolytic haloalkane dehalogenases are promising bioremediation and biocatalytic agents. Two general classes of dehalogenases have been reported from Xanthobacter and Rhodococcus. While these enzymes share 30% amino acid sequence identity, they have significantly different substrate specificities and halide-binding properties. We report the 1.5 A resolution crystal structure of the Rhodococcus dehalogenase at pH 5.5, pH 7.0, and pH 5.5 in the presence of NaI. The Rhodococcus and Xanthobacter enzymes have significant structural homology in the alpha/beta hydrolase core, but differ considerably in the cap domain. Consistent with its broad specificity for primary, secondary, and cyclic haloalkanes, the Rhodococcus enzyme has a substantially larger active site cavity. Significantly, the Rhodococcus dehalogenase has a different catalytic triad topology than the Xanthobacter enzyme. In the Xanthobacter dehalogenase, the third carboxylate functionality in the triad is provided by D260, which is positioned on the loop between beta7 and the penultimate helix. The carboxylate functionality in the Rhodococcus catalytic triad is donated from E141. A model of the enzyme cocrystallized with sodium iodide shows two iodide binding sites; one that defines the normal substrate and product-binding site and a second within the active site region. In the substrate and product complexes, the halogen binds to the Xanthobacter enzyme via hydrogen bonds with the N(eta)H of both W125 and W175. The Rhodococcusenzyme does not have a tryptophan analogous to W175. Instead, bound halide is stabilized with hydrogen bonds to the N(eta)H of W118 and to N(delta)H of N52. It appears that when cocrystallized with NaI the Rhodococcus enzyme has a rare stable S-I covalent bond to S(gamma) of C187.
+
<StructureSection load='1bn6' size='340' side='right'caption='[[1bn6]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1bn6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BN6 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]] 1.5&#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=1bn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bn6 OCA], [https://pdbe.org/1bn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bn6 RCSB], [https://www.ebi.ac.uk/pdbsum/1bn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bn6 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DHAA_RHOSD DHAA_RHOSD]
 +
== 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/bn/1bn6_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=1bn6 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1BN6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Active as [http://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] Known structural/functional Site: <scene name='pdbsite=CAT:Catalytic+Triad+Residues'>CAT</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BN6 OCA].
+
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Haloalkane dehalogenases: structure of a Rhodococcus enzyme., Newman J, Peat TS, Richard R, Kan L, Swanson PE, Affholter JA, Holmes IH, Schindler JF, Unkefer CJ, Terwilliger TC, Biochemistry. 1999 Dec 7;38(49):16105-14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10587433 10587433]
+
[[Category: Large Structures]]
-
[[Category: Haloalkane dehalogenase]]
+
[[Category: Rhodococcus sp]]
-
[[Category: Rhodococcus sp.]]
+
[[Category: Affholter JA]]
-
[[Category: Single protein]]
+
[[Category: Holmes IH]]
-
[[Category: Affholter, J A.]]
+
[[Category: Kan L]]
-
[[Category: Holmes, I H.]]
+
[[Category: Newman J]]
-
[[Category: Kan, L.]]
+
[[Category: Peat TS]]
-
[[Category: Newman, J.]]
+
[[Category: Richard R]]
-
[[Category: Peat, T S.]]
+
[[Category: Schindler JF]]
-
[[Category: Richard, R.]]
+
[[Category: Swanson PE]]
-
[[Category: Schindler, J F.]]
+
[[Category: Terwilliger TC]]
-
[[Category: Swanson, P E.]]
+
[[Category: Unkefer CJ]]
-
[[Category: Terwilliger, T C.]]
+
-
[[Category: Unkefer, C J.]]
+
-
[[Category: alpha/beta-hydrolase]]
+
-
[[Category: crystal structure]]
+
-
[[Category: dehalogenase]]
+
-
[[Category: dhla]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:56:59 2008''
+

Current revision

HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES

PDB ID 1bn6

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/1bn6"
Personal tools