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3f0o

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Revision as of 00:27, 28 December 2023

Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system

Structural highlights

3f0o is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.76Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MERB_ECOLX Cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. One product is Hg(2+), which is subsequently detoxified by the mercuric reductase (By similarity).

Evolutionary Conservation

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

Publication Abstract from PubMed

Bacteria resistant to methylmercury utilize two enzymes (MerA and MerB) to degrade methylmercury to the less toxic elemental mercury. The crucial step is the cleavage of the carbon-mercury bond of methylmercury by the organomercurial lyase (MerB). In this study, we determined high resolution crystal structures of MerB in both the free (1.76-A resolution) and mercury-bound (1.64-A resolution) states. The crystal structure of free MerB is very similar to the NMR structure, but important differences are observed when comparing the two structures. In the crystal structure, an amino-terminal alpha-helix that is not present in the NMR structure makes contact with the core region adjacent to the catalytic site. This interaction between the amino-terminal helix and the core serves to bury the active site of MerB. The crystal structures also provide detailed insights into the mechanism of carbon-mercury bond cleavage by MerB. The structures demonstrate that two conserved cysteines (Cys-96 and Cys-159) play a role in substrate binding, carbon-mercury bond cleavage, and controlled product (ionic mercury) release. In addition, the structures establish that an aspartic acid (Asp-99) in the active site plays a crucial role in the proton transfer step required for the cleavage of the carbon-mercury bond. These findings are an important step in understanding the mechanism of carbon-mercury bond cleavage by MerB.

Crystal structures of the organomercurial lyase MerB in its free and mercury-bound forms: insights into the mechanism of methylmercury degradation.,Lafrance-Vanasse J, Lefebvre M, Di Lello P, Sygusch J, Omichinski JG J Biol Chem. 2009 Jan 9;284(2):938-44. Epub 2008 Nov 12. PMID:19004822^[1]

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

References

↑ Lafrance-Vanasse J, Lefebvre M, Di Lello P, Sygusch J, Omichinski JG. Crystal structures of the organomercurial lyase MerB in its free and mercury-bound forms: insights into the mechanism of methylmercury degradation. J Biol Chem. 2009 Jan 9;284(2):938-44. Epub 2008 Nov 12. PMID:19004822 doi:10.1074/jbc.M807143200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3f0o"

@@ Line 3: / Line 3: @@
 <StructureSection load='3f0o' size='340' side='right'caption='[[3f0o]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3f0o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F0O FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3f0o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F0O FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</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]] 1.76&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s6l|1s6l]], [[3f0p|3f0p]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">merB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alkylmercury_lyase Alkylmercury lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.2 4.99.1.2] </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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [https://pdbe.org/3f0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [https://www.ebi.ac.uk/pdbsum/3f0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f0o ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MERB_ECOLX MERB_ECOLX]] Cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. One product is Hg(2+), which is subsequently detoxified by the mercuric reductase (By similarity).
+[https://www.uniprot.org/uniprot/MERB_ECOLX MERB_ECOLX] Cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. One product is Hg(2+), which is subsequently detoxified by the mercuric reductase (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Alkylmercury lyase]]
 [[Category: Large Structures]]
-[[Category: Lafrance-Vanasse, J]]
+[[Category: Di Lello P]]
-[[Category: Lefebvre, M]]
+[[Category: Lafrance-Vanasse J]]
-[[Category: Lello, P Di]]
+[[Category: Lefebvre M]]
-[[Category: Omichinski, J G]]
+[[Category: Omichinski JG]]
-[[Category: Sygusch, J]]
+[[Category: Sygusch J]]
-[[Category: Lyase]]
-[[Category: Merb]]
-[[Category: Mercuric resistance]]
-[[Category: Mercury resistance]]
-[[Category: Organomercurial lyase]]
-[[Category: Plasmid]]

3f0o

From Proteopedia

Revision as of 00:27, 28 December 2023

Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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