7qbu

From Proteopedia

(Difference between revisions)

Current revision

B12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, and S-methyl-5'-thioadenosine bound.

Structural highlights

7qbu is a 2 chain structure with sequence from Methanosarcina acetivorans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.298Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MCRAM_METAC Radical SAM methyltransferase that is responsible for the C(5)-methylation of 'Arg-285' of the methyl-coenzyme M reductase (MCR) subunit alpha McrA. This post-translational methylation, despite being not essential in vivo, plays a role for the stability and structural integrity of MCR.^[1]

Publication Abstract from PubMed

By catalysing the microbial formation of methane, methyl-coenzyme M reductase has a central role in the global levels of this greenhouse gas(1,2). The activity of methyl-coenzyme M reductase is profoundly affected by several unique post-translational modifications(3-6), such as a unique C-methylation reaction catalysed by methanogenesis marker protein 10 (Mmp10), a radical S-adenosyl-L-methionine (SAM) enzyme(7,8). Here we report the spectroscopic investigation and atomic resolution structure of Mmp10 from Methanosarcina acetivorans, a unique B12 (cobalamin)-dependent radical SAM enzyme(9). The structure of Mmp10 reveals a unique enzyme architecture with four metallic centres and critical structural features involved in the control of catalysis. In addition, the structure of the enzyme-substrate complex offers a glimpse into a B12-dependent radical SAM enzyme in a precatalytic state. By combining electron paramagnetic resonance spectroscopy, structural biology and biochemistry, our study illuminates the mechanism by which the emerging superfamily of B12-dependent radical SAM enzymes catalyse chemically challenging alkylation reactions and identifies distinctive active site rearrangements to provide a structural rationale for the dual use of the SAM cofactor for radical and nucleophilic chemistry.

Crystallographic snapshots of a B12-dependent radical SAM methyltransferase.,Fyfe CD, Bernardo-Garcia N, Fradale L, Grimaldi S, Guillot A, Brewee C, Chavas LMG, Legrand P, Benjdia A, Berteau O Nature. 2022 Feb;602(7896):336-342. doi: 10.1038/s41586-021-04355-9. Epub 2022, Feb 2. PMID:35110733^[2]

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

References

↑ Deobald D, Adrian L, Schöne C, Rother M, Layer G. Identification of a unique Radical SAM methyltransferase required for the sp(3)-C-methylation of an arginine residue of methyl-coenzyme M reductase. Sci Rep. 2018 May 9;8(1):7404. PMID:29743535 doi:10.1038/s41598-018-25716-x
↑ Fyfe CD, Bernardo-Garcia N, Fradale L, Grimaldi S, Guillot A, Brewee C, Chavas LMG, Legrand P, Benjdia A, Berteau O. Crystallographic snapshots of a B12-dependent radical SAM methyltransferase. Nature. 2022 Feb;602(7896):336-342. doi: 10.1038/s41586-021-04355-9. Epub 2022, Feb 2. PMID:35110733 doi:http://dx.doi.org/10.1038/s41586-021-04355-9

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7qbu"

@@ Line 3: / Line 3: @@
 <StructureSection load='7qbu' size='340' side='right'caption='[[7qbu]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7qbu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QBU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7qbu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_acetivorans Methanosarcina acetivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QBU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COB:CO-METHYLCOBALAMIN'>COB</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.298&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COB:CO-METHYLCOBALAMIN'>COB</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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'>[https://proteopedia.org/fgij/fg.htm?mol=7qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qbu OCA], [https://pdbe.org/7qbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qbu RCSB], [https://www.ebi.ac.uk/pdbsum/7qbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qbu ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/MCRAM_METAC MCRAM_METAC] Radical SAM methyltransferase that is responsible for the C(5)-methylation of 'Arg-285' of the methyl-coenzyme M reductase (MCR) subunit alpha McrA. This post-translational methylation, despite being not essential in vivo, plays a role for the stability and structural integrity of MCR.<ref>PMID:29743535</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Benjdia, A]]
+[[Category: Methanosarcina acetivorans]]
-[[Category: Berteau, O]]
+[[Category: Benjdia A]]
-[[Category: Chavas, L M.G]]
+[[Category: Berteau O]]
-[[Category: Fyfe, C D]]
+[[Category: Chavas LMG]]
-[[Category: Legrand, P]]
+[[Category: Fyfe CD]]
-[[Category: B12 binding]]
+[[Category: Legrand P]]
-[[Category: Metal binding protein]]
-[[Category: Methyltransferase]]
-[[Category: Radical sam]]
-[[Category: Sp3 carbon methylation]]

7qbu

From Proteopedia

Current revision

B12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, and S-methyl-5'-thioadenosine bound.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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