7VVV

Crystal structure of MmtN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Insights into methionine S-methylation in diverse organisms.

Peng, M.Li, C.Y.Chen, X.L.Williams, B.T.Li, K.Gao, Y.N.Wang, P.Wang, N.Gao, C.Zhang, S.Schoelmerich, M.C.Banfield, J.F.Miller, J.B.Le Brun, N.E.Todd, J.D.Zhang, Y.Z.

(2022) Nat Commun 13: 2947-2947

  • DOI: https://doi.org/10.1038/s41467-022-30491-5
  • Primary Citation of Related Structures:  
    7VVV, 7VVW, 7VVX

  • PubMed Abstract: 

    Dimethylsulfoniopropionate (DMSP) is an important marine anti-stress compound, with key roles in global nutrient cycling, chemotaxis and, potentially, climate regulation. Recently, diverse marine Actinobacteria, α- and γ-proteobacteria were shown to initiate DMSP synthesis via the methionine (Met) S-methyltransferase enzyme (MmtN), generating S-methyl-Met (SMM). Here we characterize a roseobacterial MmtN, providing structural and mechanistic insights into this DMSP synthesis enzyme. We propose that MmtN uses the proximity and desolvation mechanism for Met S-methylation with two adjacent MmtN monomers comprising the Met binding site. We also identify diverse functional MmtN enzymes in potentially symbiotic archaeal Candidatus Woesearchaeota and Candidate Phyla Radiation (CPR) bacteria, and the animalcule Adineta steineri, not anticipated to produce SMM and/or DMSP. These diverse MmtN enzymes, alongside the larger plant MMT enzyme with an N-terminus homologous to MmtN, likely utilize the same proximity and desolvation mechanism. This study provides important insights into the catalytic mechanism of SMM and/or DMSP production, and proposes roles for these compounds in secondary metabolite production, and SMM cycling in diverse organisms and environments.


  • Organizational Affiliation

    Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SAM-dependent methyltransferase
A, B, C
305Roseovarius indicusMutation(s): 3 
Gene Names: XM52_07085
UniProt
Find proteins for A0A0T5PCK9 (Roseovarius indicus)
Explore A0A0T5PCK9 
Go to UniProtKB:  A0A0T5PCK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0T5PCK9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.734α = 90
b = 131.277β = 90
c = 134.465γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31630012
National Science Foundation (NSF, China)ChinaU1706207
National Science Foundation (NSF, China)China91851205
National Science Foundation (NSF, China)China42076229
National Science Foundation (NSF, China)China31800107
National Science Foundation (NSF, China)China41706152
National Science Foundation (NSF, China)China42106142

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references