1mj5: Difference between revisions

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-[[Image:1mj5.gif|left|200px]]
- {{Structure
+==LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution==
-|PDB= 1mj5 |SIZE=350|CAPTION= <scene name='initialview01'>1mj5</scene>, resolution 0.950&Aring;
+<StructureSection load='1mj5' size='340' side='right'caption='[[1mj5]], [[Resolution|resolution]] 0.95&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=CL:CHLORIDE ION'>CL</scene>
+<table><tr><td colspan='2'>[[1mj5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MJ5 FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.95&#8491;</td></tr>
-|GENE= LINB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13689 Sphingomonas paucimobilis])
+<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=MG:MAGNESIUM+ION'>MG</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=1mj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mj5 OCA], [https://pdbe.org/1mj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mj5 RCSB], [https://www.ebi.ac.uk/pdbsum/1mj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mj5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LINB_SPHJU LINB_SPHJU] 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 since not only monochloroalkanes (C3 to C10) but also dichloroalkanes (> C3), bromoalkanes, and chlorinated aliphatic alcohols are good substrates (PubMed:9293022, PubMed:10100638). Shows almost no activity with 1,2-dichloroethane, but very high activity with the brominated analog (PubMed:9293022). Is involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane (gamma-HCH or lindane) as it also catalyzes conversion of 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN) to 2,5-dichloro-2,5-cyclohexadiene-1,4-diol (2,5-DDOL) via the intermediate 2,4,5-trichloro-2,5-cyclohexadiene-1-ol (2,4,5-DNOL) (PubMed:7691794). This degradation pathway allows S.japonicum UT26 to grow on gamma-HCH as the sole source of carbon and energy.<ref>PMID:10100638</ref> <ref>PMID:7691794</ref> <ref>PMID:9293022</ref>
+== 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/mj/1mj5_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=1mj5 ConSurf].
+<div style="clear:both"></div>
-'''LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution'''
+==See Also==
+*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
+== References ==
-==Overview==
+<references/>
-We present the structure of LinB, a 33-kDa haloalkane dehalogenase from Sphingomonas paucimobilis UT26, at 0.95 A resolution. The data have allowed us to directly observe the anisotropic motions of the catalytic residues. In particular, the side-chain of the catalytic nucleophile, Asp108, displays a high degree of disorder. It has been modeled in two conformations, one similar to that observed previously (conformation A) and one strained (conformation B) that approached the catalytic base (His272). The strain in conformation B was mainly in the C(alpha)-C(beta)-C(gamma) angle (126 degrees ) that deviated by 13.4 degrees from the "ideal" bond angle of 112.6 degrees. On the basis of these observations, we propose a role for the charge state of the catalytic histidine in determining the geometry of the catalytic residues. We hypothesized that double-protonation of the catalytic base (His272) reduces the distance between the side-chain of this residue and that of the Asp108. The results of molecular dynamics simulations were consistent with the structural data showing that protonation of the His272 side-chain nitrogen atoms does indeed reduce the distance between the side-chains of the residues in question, although the simulations failed to demonstrate the same degree of strain in the Asp108 C(alpha)-C(beta)-C(gamma) angle. Instead, the changes in the molecular dynamics structures were distributed over several bond and dihedral angles. Quantum mechanics calculations on LinB with 1-chloro-2,2-dimethylpropane as a substrate were performed to determine which active site conformations and protonation states were most likely to result in catalysis. It was shown that His272 singly protonated at N(delta)(1) and Asp108 in conformation A gave the most exothermic reaction (DeltaH = -22 kcal/mol). With His272 doubly protonated at N(delta)(1) and N(epsilon)(2), the reactions were only slightly exothermic or were endothermic. In all calculations starting with Asp108 in conformation B, the Asp108 C(alpha)-C(beta)-C(gamma) angle changed during the reaction and the Asp108 moved to conformation A. The results presented here indicate that the positions of the catalytic residues and charge state of the catalytic base are important for determining reaction energetics in LinB.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-MJ5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MJ5 OCA].
-==Reference==
-Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues., Oakley AJ, Klvana M, Otyepka M, Nagata Y, Wilce MC, Damborsky J, Biochemistry. 2004 Feb 3;43(4):870-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14744129 14744129]
-[[Category: Haloalkane dehalogenase]]
-[[Category: Single protein]]
 [[Category: Sphingomonas paucimobilis]]
-[[Category: Damborsky, J.]]
+[[Category: Damborsky J]]
-[[Category: Oakley, A J.]]
+[[Category: Oakley AJ]]
-[[Category: Wilce, M C.]]
+[[Category: Wilce MC]]
-[[Category: CL]]
-[[Category: MG]]
-[[Category: 1]]
-[[Category: 3]]
-[[Category: 4]]
-[[Category: 4-cyclohexadiene dehalogenase]]
-[[Category: 6-tetrachloro-1]]
-[[Category: alpha/beta-hydrolase]]
-[[Category: gamma-hexachlorocyclohexane degradation]]
-[[Category: haloalkane dehalogenase]]
-[[Category: hydrolase]]
-[[Category: linb]]
-[[Category: ultra high resolution]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:44:01 2008''