XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase.

Crystallography, X-Ray Lasers Methane / chemistry Oxidation-Reduction Oxidoreductases Temperature
Methanogens Nickel Serial femtosecond crystallography (SFX) X-ray Diffraction (XRD) X-ray Emission Spectroscopy (XES) X-ray Free-Electron Laser (XFEL)

Journal

Journal of inorganic biochemistry
ISSN: 1873-3344
Titre abrégé: J Inorg Biochem
Pays: United States
ID NLM: 7905788

Informations de publication

Date de publication:
05 2022
Historique:
received: 10 11 2021
revised: 10 02 2022
accepted: 10 02 2022
pubmed: 25 2 2022
medline: 6 5 2022
entrez: 24 2 2022
Statut: ppublish

Résumé

Methyl-Coenzyme M Reductase (MCR) catalyzes the biosynthesis of methane in methanogenic archaea, using a catalytic Ni-centered Cofactor F430 in its active site. It also catalyzes the reverse reaction, that is, the anaerobic activation and oxidation, including the cleavage of the CH bond in methane. Because methanogenesis is the major source of methane on earth, understanding the reaction mechanism of this enzyme can have massive implications in global energy balances. While recent publications have proposed a radical-based catalytic mechanism as well as novel sulfonate-based binding modes of MCR for its native substrates, the structure of the active state of MCR, as well as a complete characterization of the reaction, remain elusive. Previous attempts to structurally characterize the active MCR-Ni(I) state have been unsuccessful due to oxidation of the redox- sensitive catalytic Ni center. Further, while many cryo structures of the inactive Ni(II)-enzyme in various substrates-bound forms have been published, no room temperature structures have been reported, and the structure and mechanism of MCR under physiologically relevant conditions is not known. In this study, we report the first room temperature structure of the MCRred1-silent Ni(II) form using an X-ray Free-Electron Laser (XFEL), with simultaneous X-ray Emission Spectroscopy (XES) and X-ray Diffraction (XRD) data collection. In celebration of the seminal contributions of inorganic chemist Dick Holm to our understanding of nickel-based catalysis, we are honored to announce our findings in this special issue dedicated to this remarkable pioneer of bioinorganic chemistry.

Identifiants

DOI: 10.1016/j.jinorgbio.2022.111768 PMID: 35202981 PMC: PMC8930625
pubmed: 35202981
pii: S0162-0134(22)00057-5
doi: 10.1016/j.jinorgbio.2022.111768
pmc: PMC8930625
mid: NIHMS1783308
pii:
doi:

Substances chimiques

Oxidoreductases EC 1.-
methyl coenzyme M reductase EC 2.8.4.1
Methane OP0UW79H66

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

111768

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM126289
Pays : United States
Organisme : NIGMS NIH HHS
ID : R56 GM055302
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM126982
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM110501
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM117126
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM055302
Pays : United States
Organisme : NIGMS NIH HHS
ID : P30 GM124169
Pays : United States
Organisme : NIH HHS
ID : S10 OD023453
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM139687
Pays : United States
Organisme : NIGMS NIH HHS
ID : P01 GM063210
Pays : United States

Informations de copyright

Copyright © 2022 Elsevier Inc. All rights reserved.

Références

Eur J Biochem. 1986 Apr 1;156(1):171-7
pubmed: 3082633
Nature. 2011 Nov 27;481(7379):98-101
pubmed: 22121022
Science. 2021 Jul 2;373(6550):118-121
pubmed: 34210888
J Am Chem Soc. 2009 Jul 29;131(29):9912-3
pubmed: 19569621
Protein Sci. 2021 Jan;30(1):70-82
pubmed: 32881101
Nat Commun. 2021 Jul 22;12(1):4461
pubmed: 34294694
J Am Chem Soc. 2011 Apr 20;133(15):5626-8
pubmed: 21438550
Science. 2016 Dec 23;354(6319):1552-1557
pubmed: 28008064
Elife. 2013 Sep 10;2:e01456
pubmed: 24040512
Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):237-42
pubmed: 24363322
Rev Sci Instrum. 2012 Jul;83(7):073114
pubmed: 22852678
Biochemistry. 2019 Dec 31;58(52):5198-5220
pubmed: 30951290
Science. 1997 Nov 21;278(5342):1457-62
pubmed: 9367957
Nat Methods. 2017 Apr;14(4):443-449
pubmed: 28250468
Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):877-894
pubmed: 30198898
Nat Methods. 2014 May;11(5):545-8
pubmed: 24633409
Nature. 2021 Aug;596(7871):171-172
pubmed: 34373637
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):282-92
pubmed: 21460446
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
Science. 2016 May 20;352(6288):953-8
pubmed: 27199421
J Biol Chem. 2015 Apr 10;290(15):9322-34
pubmed: 25691570
Angew Chem Int Ed Engl. 2016 Aug 26;55(36):10630-3
pubmed: 27467699
Microbiology (Reading). 1998 Sep;144 ( Pt 9):2377-2406
pubmed: 9782487
ACS Med Chem Lett. 2018 Jun 18;9(9):878-883
pubmed: 30258534
Front Microbiol. 2013 Apr 01;4:69
pubmed: 23554601
J Synchrotron Radiat. 2019 Mar 1;26(Pt 2):346-357
pubmed: 30855242
Methods Enzymol. 1997;276:307-26
pubmed: 27754618
Biochemistry. 2010 Sep 7;49(35):7683-93
pubmed: 20707311
Sci Adv. 2021 Aug 20;7(34):
pubmed: 34417180
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
pubmed: 20383002
Biochemistry. 2018 Aug 7;57(31):4629-4637
pubmed: 29906115
J Biol Chem. 2006 Nov 10;281(45):34663-76
pubmed: 16966321
Bioinformatics. 2018 Oct 15;34(20):3586-3588
pubmed: 29741570
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67
pubmed: 22505256
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
pubmed: 15572765
Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877
pubmed: 31588918
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
pubmed: 20124702
Nucleic Acids Res. 2019 Jul 2;47(W1):W636-W641
pubmed: 30976793
Nat Commun. 2017 Sep 14;8(1):542
pubmed: 28912485
J Mol Biol. 2001 May 25;309(1):315-30
pubmed: 11491299
Sci Rep. 2018 Feb 13;8(1):2913
pubmed: 29440727
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
pubmed: 19461840
Nature. 2014 Mar 27;507(7493):488-91
pubmed: 24670769
J Am Chem Soc. 2021 Apr 14;143(14):5481-5496
pubmed: 33761259
Elife. 2017 Sep 07;6:
pubmed: 28880150
Acta Crystallogr D Struct Biol. 2018 Feb 1;74(Pt 2):85-97
pubmed: 29533234

Auteurs

Christopher J Ohmer (CJ)

Department of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Dr., 5200 MSRBIII, Ann Arbor, MI 48109-0606, USA.

Medhanjali Dasgupta (M)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Anjali Patwardhan (A)

Department of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Dr., 5200 MSRBIII, Ann Arbor, MI 48109-0606, USA.

Isabel Bogacz (I)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Corey Kaminsky (C)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Margaret D Doyle (MD)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Percival Yang-Ting Chen (PY)

Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

Stephen M Keable (SM)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Hiroki Makita (H)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Philipp S Simon (PS)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Ramzi Massad (R)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.

Thomas Fransson (T)

Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden.

Ruchira Chatterjee (R)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Asmit Bhowmick (A)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Daniel W Paley (DW)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Nigel W Moriarty (NW)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Aaron S Brewster (AS)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Leland B Gee (LB)

LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.

Roberto Alonso-Mori (R)

LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.

Frank Moss (F)

LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.

Franklin D Fuller (FD)

LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.

Alexander Batyuk (A)

LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.

Nicholas K Sauter (NK)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Uwe Bergmann (U)

Department of Physics, University of Wisconsin-Madison, Madison, WI 53706, USA.

Catherine L Drennan (CL)

Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Department of Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Canadian Institute for Advanced Research, Bio-inspired Solar Energy Program, Toronto, ON M5G 1M1, Canada.

Vittal K Yachandra (VK)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Junko Yano (J)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: jyano@lbl.gov.

Jan F Kern (JF)

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: jfkern@lbl.gov.

Stephen W Ragsdale (SW)

Department of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Dr., 5200 MSRBIII, Ann Arbor, MI 48109-0606, USA. Electronic address: sragsdal@umich.edu.

Articles similaires

A molecular mechanism for bright color variation in parrots.

Roberto Arbore, Soraia Barbosa, Jindich Brejcha et al.
1.00
Animals Feathers Pigmentation Parrots Aldehyde Dehydrogenase

Determination of reasonable ice amount in foam box of pasteurized milk under air logistics mode.

Shemiao Feng
1.00
Animals Milk Ice Pasteurization Transportation

Harnessing Limestone powder to enhance the thermal crack resistance of manufactured sand.

Xinting Liu, Jianda Xin, Ying Liu et al.
1.00
Calcium Carbonate Sand Powders Construction Materials Materials Testing

Tumor-targeted glutathione oxidation catalysis with ruthenium nanoreactors against hypoxic osteosarcoma.

Hanchen Zhang, Nicolás Montesdeoca, Dongsheng Tang et al.
1.00
Osteosarcoma Animals Glutathione Oxidation-Reduction Mice

Classifications MeSH

questionsmedicales.fr › Techniques d'investigation › Techniques de chimie analytique › Cristallographie aux rayons X › XFEL serial crystallography reveals the room...
questionsmedicales.fr › Équipement et fournitures › Équipement et fournitures pour les applications des radiations › Lasers › XFEL serial crystallography reveals the room...
questionsmedicales.fr › Composés chimiques organiques › Hydrocarbures › Hydrocarbures acycliques › Alcanes › Méthane › XFEL serial crystallography reveals the room...
questionsmedicales.fr › Métabolisme › Métabolisme énergétique › Oxydoréduction › XFEL serial crystallography reveals the room...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Oxidoreductases › XFEL serial crystallography reveals the room...
questionsmedicales.fr › Environnement et santé publique › Environnement › Concepts météorologiques › Atmosphère › Temps (météorologie) › Température › XFEL serial crystallography reveals the room...