1mj5: Difference between revisions

Latest revision as of 07:44, 14 February 2024

LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution

Structural highlights

1mj5 is a 1 chain structure with sequence from Sphingomonas paucimobilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 0.95Å
Ligands:	CL, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3]

Evolutionary Conservation

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

References

↑ Hynková K, Nagata Y, Takagi M, Damborský J. Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. FEBS Lett. 1999 Mar 5;446(1):177-81. PMID:10100638 doi:10.1016/s0014-5793(99)00199-4
↑ Nagata Y, Nariya T, Ohtomo R, Fukuda M, Yano K, Takagi M. Cloning and sequencing of a dehalogenase gene encoding an enzyme with hydrolase activity involved in the degradation of gamma-hexachlorocyclohexane in Pseudomonas paucimobilis. J Bacteriol. 1993 Oct;175(20):6403-10. PMID:7691794 doi:10.1128/jb.175.20.6403-6410.1993
↑ Nagata Y, Miyauchi K, Damborsky J, Manova K, Ansorgova A, Takagi M. Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26. Appl Environ Microbiol. 1997 Sep;63(9):3707-10. PMID:9293022 doi:10.1128/aem.63.9.3707-3710.1997

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Hynková K, Nagata Y, Takagi M, Damborský J. Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. FEBS Lett. 1999 Mar 5;446(1):177-81. PMID:10100638 doi:10.1016/s0014-5793(99)00199-4

[2] Nagata Y, Nariya T, Ohtomo R, Fukuda M, Yano K, Takagi M. Cloning and sequencing of a dehalogenase gene encoding an enzyme with hydrolase activity involved in the degradation of gamma-hexachlorocyclohexane in Pseudomonas paucimobilis. J Bacteriol. 1993 Oct;175(20):6403-10. PMID:7691794 doi:10.1128/jb.175.20.6403-6410.1993

[3] Nagata Y, Miyauchi K, Damborsky J, Manova K, Ansorgova A, Takagi M. Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26. Appl Environ Microbiol. 1997 Sep;63(9):3707-10. PMID:9293022 doi:10.1128/aem.63.9.3707-3710.1997

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-[[Image:1mj5.png|left|200px]]
-{{STRUCTURE_1mj5|  PDB=1mj5  |  SCENE=  }}
+==LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution==
+<StructureSection load='1mj5' size='340' side='right'caption='[[1mj5]], [[Resolution|resolution]] 0.95&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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]]
-{{ABSTRACT_PUBMED_14744129}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[1mj5]] is a 1 chain structure with 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].
+</StructureSection>
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:014744129</ref><ref group="xtra">PMID:018754631</ref><references group="xtra"/>
-[[Category: Haloalkane dehalogenase]]
 [[Category: Sphingomonas paucimobilis]]
-[[Category: Damborsky, J.]]
+[[Category: Damborsky J]]
-[[Category: Oakley, A J.]]
+[[Category: Oakley AJ]]
-[[Category: Wilce, M C.]]
+[[Category: Wilce MC]]
-[[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]]

1mj5: Difference between revisions

Latest revision as of 07:44, 14 February 2024

LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution

Structural highlights

Function

Evolutionary Conservation

See Also

References

Contents

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