5G0R

METHYL-COENZYME M REDUCTASE I FROM METHANOTHERMOBACTER MARBURGENSIS EXPOSED TO 3-NITROOXYPROPANOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Mode of Action Uncovered for the Specific Reduction of Methane Emissions from Ruminants by the Small Molecule 3-Nitrooxypropanol.

Duin, E.C.Wagner, T.Shima, S.Prakash, D.Cronin, B.Yanez-Ruiz, D.R.Duval, S.Rumbeli, R.Stemmler, R.T.Thauer, R.K.Kindermann, M.

(2016) Proc Natl Acad Sci U S A 113: 6172

  • DOI: 10.1073/pnas.1600298113
  • Primary Citation of Related Structures:  
    5G0R

  • PubMed Abstract: 
  • Ruminants, such as cows, sheep, and goats, predominantly ferment in their rumen plant material to acetate, propionate, butyrate, CO2, and methane. Whereas the short fatty acids are absorbed and metabolized by the animals, the greenhouse gas methane escapes via eructation and breathing of the animals into the atmosphere ...

    Ruminants, such as cows, sheep, and goats, predominantly ferment in their rumen plant material to acetate, propionate, butyrate, CO2, and methane. Whereas the short fatty acids are absorbed and metabolized by the animals, the greenhouse gas methane escapes via eructation and breathing of the animals into the atmosphere. Along with the methane, up to 12% of the gross energy content of the feedstock is lost. Therefore, our recent report has raised interest in 3-nitrooxypropanol (3-NOP), which when added to the feed of ruminants in milligram amounts persistently reduces enteric methane emissions from livestock without apparent negative side effects [Hristov AN, et al. (2015) Proc Natl Acad Sci USA 112(34):10663-10668]. We now show with the aid of in silico, in vitro, and in vivo experiments that 3-NOP specifically targets methyl-coenzyme M reductase (MCR). The nickel enzyme, which is only active when its Ni ion is in the +1 oxidation state, catalyzes the methane-forming step in the rumen fermentation. Molecular docking suggested that 3-NOP preferably binds into the active site of MCR in a pose that places its reducible nitrate group in electron transfer distance to Ni(I). With purified MCR, we found that 3-NOP indeed inactivates MCR at micromolar concentrations by oxidation of its active site Ni(I). Concomitantly, the nitrate ester is reduced to nitrite, which also inactivates MCR at micromolar concentrations by oxidation of Ni(I). Using pure cultures, 3-NOP is demonstrated to inhibit growth of methanogenic archaea at concentrations that do not affect the growth of nonmethanogenic bacteria in the rumen.


    Organizational Affiliation

    Research and Development, DSM Nutritional Products, 4002 Basel, Switzerland thauer@mpi-marburg.mpg.de maik.kindermann@dsm.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE I SUBUNIT ALPHAA, D550Methanothermobacter marburgensisMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for P11558 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore P11558 
Go to UniProtKB:  P11558
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11558
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE I SUBUNIT BETAB, E443Methanothermobacter marburgensisMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for P11560 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore P11560 
Go to UniProtKB:  P11560
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11560
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMAC, F249Methanothermobacter marburgensisMutation(s): 0 
EC: 2.8.4.1
UniProt
Find proteins for P11562 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore P11562 
Go to UniProtKB:  P11562
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11562
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F43
Query on F43

Download Ideal Coordinates CCD File 
I [auth A],
Y [auth D]
FACTOR 430
C42 H51 N6 Ni O13
XLFIRMYGVLUNOY-SXMZNAGASA-M
 Ligand Interaction
TP7
Query on TP7

Download Ideal Coordinates CCD File 
J [auth A],
Z [auth D]
Coenzyme B
C11 H22 N O7 P S
JBJSVEVEEGOEBZ-SCZZXKLOSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
Q [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth E],
R [auth A],
U [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D],
CA [auth D],
DA [auth E],
EA [auth E],
FA [auth E],
AA [auth D],
CA [auth D],
DA [auth E],
EA [auth E],
FA [auth E],
G [auth A],
H [auth A],
HA [auth E],
IA [auth F],
K [auth A],
L [auth A],
N [auth A],
O [auth A],
S [auth B],
T [auth B],
V [auth C],
W [auth C],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth D],
M [auth A],
P [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
AGM
Query on AGM
A, D L-PEPTIDE LINKINGC7 H17 N4 O2ARG
DYA
Query on DYA
A, D L-PEPTIDE LINKINGC4 H5 N O4ASP
GL3
Query on GL3
A, D L-PEPTIDE LINKINGC2 H5 N O SGLY
MGN
Query on MGN
A, D L-PEPTIDE LINKINGC6 H12 N2 O3GLN
MHS
Query on MHS
A, D L-PEPTIDE LINKINGC7 H11 N3 O2HIS
SMC
Query on SMC
A, D L-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.2α = 90
b = 118.101β = 92.03
c = 122.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-04-13 
  • Deposition Author(s): Wagner, T.

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2016-05-18
    Changes: Database references
  • Version 1.3: 2016-06-15
    Changes: Database references
  • Version 1.4: 2017-03-29
    Changes: Non-polymer description
  • Version 2.0: 2019-04-24
    Changes: Data collection, Derived calculations, Polymer sequence
  • Version 2.1: 2019-05-15
    Changes: Data collection, Experimental preparation