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5m8u

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PCE reductive dehalogenase from S. multivorans in complex with 4-bromophenol

Structural highlights

5m8u is a 2 chain structure with sequence from Sulfurospirillum multivorans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PCEA_SULMU Catalyzes the reductive dechlorination of tetrachloroethene (PCE) to trichloroethene (TCE) and of trichloroethene to cis-1,2-dichloroethene (DCE) (PubMed:8663199, PubMed:11976751, PubMed:12420164, PubMed:24433392, PubMed:28671181). In addition, trans-1,3-dichloropropene, 1,1,3-trichloropropene and 2,3-dichloropropene are reduced to a mixture of mono-chloropropenes, 1,1-dichloropropene, and 2-chloropropene, respectively (PubMed:11976751). Is also able to convert brominated phenols such as 4-bromophenol (4-BP), 2,4-dibromophenol (2,4-DBP) and 2,4,6-tribromophenol (2,4,6-TBP) (PubMed:28671181). Utilizes formate or pyruvate as electron donors (PubMed:16802174, PubMed:24433392). Titanium(III) citrate could also serve as electron donor (PubMed:11976751). Reduced methyl viologen can act as the artificial electron donor (PubMed:8663199, PubMed:11976751, PubMed:12420164).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

The capacity of metal-containing porphyrinoids to mediate reductive dehalogenation is implemented in cobamide-containing reductive dehalogenases (RDases), which serve as terminal reductases in organohalide-respiring microbes. RDases allow for the exploitation of halogenated compounds as electron acceptors. Their reaction mechanism is under debate. Here we report on substrate-enzyme interactions in a tetrachloroethene RDase (PceA) that also converts aryl halides. The shape of PceA's highly apolar active site directs binding of bromophenols at some distance from the cobalt and with the hydroxyl substituent towards the metal. A close cobalt-substrate interaction is not observed by electron paramagnetic resonance spectroscopy. Nonetheless, a halogen substituent para to the hydroxyl group is reductively eliminated and the path of the leaving halide is traced in the structure. Based on these findings, an enzymatic mechanism relying on a long-range electron transfer is concluded, which is without parallel in vitamin B12-dependent biochemistry and represents an effective mode of RDase catalysis.

Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer.,Kunze C, Bommer M, Hagen WR, Uksa M, Dobbek H, Schubert T, Diekert G Nat Commun. 2017 Jul 3;8:15858. doi: 10.1038/ncomms15858. PMID:28671181^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Neumann A, Siebert A, Trescher T, Reinhardt S, Wohlfarth G, Diekert G. Tetrachloroethene reductive dehalogenase of Dehalospirillum multivorans: substrate specificity of the native enzyme and its corrinoid cofactor. Arch Microbiol. 2002 May;177(5):420-6. PMID:11976751 doi:10.1007/s00203-002-0409-3
↑ Siebert A, Neumann A, Schubert T, Diekert G. A non-dechlorinating strain of Dehalospirillum multivorans: evidence for a key role of the corrinoid cofactor in the synthesis of an active tetrachloroethene dehalogenase. Arch Microbiol. 2002 Dec;178(6):443-9. PMID:12420164 doi:10.1007/s00203-002-0473-8
↑ John M, Schmitz RP, Westermann M, Richter W, Diekert G. Growth substrate dependent localization of tetrachloroethene reductive dehalogenase in Sulfurospirillum multivorans. Arch Microbiol. 2006 Aug;186(2):99-106. PMID:16802174 doi:10.1007/s00203-006-0125-5
↑ Keller S, Ruetz M, Kunze C, Kräutler B, Diekert G, Schubert T. Exogenous 5,6-dimethylbenzimidazole caused production of a non-functional tetrachloroethene reductive dehalogenase in Sulfurospirillum multivorans. Environ Microbiol. 2014 Nov;16(11):3361-9. PMID:24433392 doi:10.1111/1462-2920.12268
↑ Kunze C, Bommer M, Hagen WR, Uksa M, Dobbek H, Schubert T, Diekert G. Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer. Nat Commun. 2017 Jul 3;8:15858. doi: 10.1038/ncomms15858. PMID:28671181 doi:http://dx.doi.org/10.1038/ncomms15858
↑ Neumann A, Wohlfarth G, Diekert G. Purification and characterization of tetrachloroethene reductive dehalogenase from Dehalospirillum multivorans. J Biol Chem. 1996 Jul 12;271(28):16515-9. PMID:8663199 doi:10.1074/jbc.271.28.16515
↑ Kunze C, Bommer M, Hagen WR, Uksa M, Dobbek H, Schubert T, Diekert G. Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer. Nat Commun. 2017 Jul 3;8:15858. doi: 10.1038/ncomms15858. PMID:28671181 doi:http://dx.doi.org/10.1038/ncomms15858

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5m8u"

@@ Line 3: / Line 3: @@
 <StructureSection load='5m8u' size='340' side='right'caption='[[5m8u]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5m8u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfurospirillum_multivorans Sulfurospirillum multivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M8U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5M8U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5m8u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurospirillum_multivorans Sulfurospirillum multivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M8U FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=BVQ:NORPSEUDO-B12'>BVQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5m2g|5m2g]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BML:4-BROMOPHENOL'>BML</scene>, <scene name='pdbligand=BVQ:NORPSEUDO-B12'>BVQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5m8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m8u OCA], [http://pdbe.org/5m8u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m8u RCSB], [http://www.ebi.ac.uk/pdbsum/5m8u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m8u ProSAT]</span></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=5m8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m8u OCA], [https://pdbe.org/5m8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m8u RCSB], [https://www.ebi.ac.uk/pdbsum/5m8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m8u ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PCEA_SULMU PCEA_SULMU] Catalyzes the reductive dechlorination of tetrachloroethene (PCE) to trichloroethene (TCE) and of trichloroethene to cis-1,2-dichloroethene (DCE) (PubMed:8663199, PubMed:11976751, PubMed:12420164, PubMed:24433392, PubMed:28671181). In addition, trans-1,3-dichloropropene, 1,1,3-trichloropropene and 2,3-dichloropropene are reduced to a mixture of mono-chloropropenes, 1,1-dichloropropene, and 2-chloropropene, respectively (PubMed:11976751). Is also able to convert brominated phenols such as 4-bromophenol (4-BP), 2,4-dibromophenol (2,4-DBP) and 2,4,6-tribromophenol (2,4,6-TBP) (PubMed:28671181). Utilizes formate or pyruvate as electron donors (PubMed:16802174, PubMed:24433392). Titanium(III) citrate could also serve as electron donor (PubMed:11976751). Reduced methyl viologen can act as the artificial electron donor (PubMed:8663199, PubMed:11976751, PubMed:12420164).<ref>PMID:11976751</ref> <ref>PMID:12420164</ref> <ref>PMID:16802174</ref> <ref>PMID:24433392</ref> <ref>PMID:28671181</ref> <ref>PMID:8663199</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 28: @@
 [[Category: Large Structures]]
 [[Category: Sulfurospirillum multivorans]]
-[[Category: Bommer, M]]
+[[Category: Bommer M]]
-[[Category: Diekert, G]]
+[[Category: Diekert G]]
-[[Category: Dobbek, H]]
+[[Category: Dobbek H]]
-[[Category: Hagen, W R]]
+[[Category: Hagen WR]]
-[[Category: Kunze, C]]
+[[Category: Kunze C]]
-[[Category: Schubert, T]]
+[[Category: Schubert T]]
-[[Category: Uksa, M]]
+[[Category: Uksa M]]
-[[Category: Organohalide respiration anaerobic crystallisation cobalamin]]
-[[Category: Oxidoreductase]]

5m8u

From Proteopedia

Current revision

PCE reductive dehalogenase from S. multivorans in complex with 4-bromophenol

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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