Evidence map›Paper›PMID 35202981›Full record

ArticleJournal of inorganic biochemistry2022

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

Christopher J Ohmer, Medhanjali Dasgupta, Anjali Patwardhan, Isabel Bogacz, Corey Kaminsky, Margaret D Doyle, Percival Yang-Ting Chen, Stephen M Keable, Hiroki Makita, Philipp S Simon and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of inorganic biochemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed.

  1. Article
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  5. bioRxiv : the preprint server for biology · 2025
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

29 authors.

Christopher J OhmerDepartment of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Dr., 5200 MSRBIII, Ann Arbor, MI 48109-0606, USA.
Medhanjali DasguptaMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Anjali PatwardhanDepartment of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Dr., 5200 MSRBIII, Ann Arbor, MI 48109-0606, USA.
Isabel BogaczMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Corey KaminskyMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Margaret D DoyleMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Percival Yang-Ting ChenDepartment of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
Stephen M KeableMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Hiroki MakitaMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Philipp S SimonMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Ramzi MassadMolecular 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 FranssonDepartment of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden.
Ruchira ChatterjeeMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Asmit BhowmickMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Daniel W PaleyMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Nigel W MoriartyMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Aaron S BrewsterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Leland B GeeLCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Roberto Alonso-MoriLCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Frank MossLCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Franklin D FullerLCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Alexander BatyukLCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Nicholas K SauterMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Uwe BergmannDepartment of Physics, University of Wisconsin-Madison, Madison, WI 53706, USA.
Catherine L DrennanDepartment 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 YachandraMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Junko YanoMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: jyano@lbl.gov.
Jan F KernMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: jfkern@lbl.gov.
Stephen W RagsdaleDepartment 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.

Funding

PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDSP01GM063210 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI ADAMS, PAUL DAVID · 2001 to 2021
$33.5M
User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS, Gregory L Hura · 2017 to 2026
$28.6M
Taking Snapshots of the Water-Oxidation Reaction by the Mn4Ca Oxygen-Evolving Complex Using X-ray Crystallography and SpectroscopyR01GM055302 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI YACHANDRA, VITTAL · 1997 to 2022
$9.1M
Structural Dynamics at LCLSP41GM139687 · NIGMS · STANFORD UNIVERSITY · PI BOUTET, SEBASTIEN · 2021 to 2025
$7.5M
DIALS: New Computational Methods to Enable Challenging Crystallographic ExperimentsR01GM117126 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI SAUTER, NICHOLAS K · 2016 to 2023
$6.1M
Biological Spectroscopy and Crystallography Using an X-ray Free Electron Laser - Supplemental EquipmentR01GM110501 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI Junko Yano · 2014 to 2026
$4.8M
High throughput sample delivery method for time resolved studies of enzyme reactions with X-ray and complementary techniquesR01GM126289 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI KERN, JAN F · 2017 to 2025
$4.6M
Metalloenzyme structure, function and assemblyR35GM126982 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI CATHERINE L DRENNAN · 2018 to 2026
$3.4M
High-end X-ray Detector System for Femtosecond CrystallographyS10OD023453 · OD · STANFORD UNIVERSITY · PI BOUTET, SEBASTIEN · 2017 to 2017
$1.7M
Structure and Function of the Mn Oxygen-Evolving ComplexR56GM055302 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI YACHANDRA, VITTAL · 2009 to 2009
$530k
NIGMS NIH HHS P01 GM063210NIGMS NIH HHS P30 GM124169NIGMS NIH HHS P41 GM139687NIGMS NIH HHS R01 GM055302NIGMS NIH HHS R01 GM110501NIGMS NIH HHS R01 GM117126NIGMS NIH HHS R01 GM126289NIGMS NIH HHS R35 GM126982NIGMS NIH HHS R56 GM055302NIH HHS S10 OD023453
6 · The paper itself

Abstract

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.

Indexed as

LasersMethaneCrystallography, X-RayOxidation-ReductionOxidoreductasesTemperatureMethanemethyl coenzyme M reductaseOxidoreductasesMethanogensNickelSerial femtosecond crystallography (SFX)X-ray Diffraction (XRD)X-ray Emission Spectroscopy (XES)X-ray Free-Electron Laser (XFEL)

Identifiers

PMID35202981
PMCPMC8930625

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.