6B9T

Crystal structure of MPnS with substrate 2-hydroxyethylphosphonate (2-HEP) and Fe(II) bound

  • Classification: OXIDOREDUCTASE
  • Organism(s): Nitrosopumilus maritimus SCM1
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-10-11 Released: 2017-12-20 
  • Deposition Author(s): Born, D.A., Drennan, C.L.
  • Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for methylphosphonate biosynthesis.

Born, D.A.Ulrich, E.C.Ju, K.S.Peck, S.C.van der Donk, W.A.Drennan, C.L.

(2017) Science 358: 1336-1339

  • DOI: https://doi.org/10.1126/science.aao3435
  • Primary Citation of Related Structures:  
    6B9R, 6B9S, 6B9T

  • PubMed Abstract: 

    Methylphosphonate synthase (MPnS) produces methylphosphonate, a metabolic precursor to methane in the upper ocean. Here, we determine a 2.35-angstrom resolution structure of MPnS and discover that it has an unusual 2-histidine-1-glutamine iron-coordinating triad. We further solve the structure of a related enzyme, hydroxyethylphosphonate dioxygenase from Streptomyces albus ( Sa HEPD), and find that it displays the same motif. Sa HEPD can be converted into an MPnS by mutation of glutamine-adjacent residues, identifying the molecular requirements for methylphosphonate synthesis. Using these sequence markers, we find numerous putative MPnSs in marine microbiomes and confirm that MPnS is present in the abundant Pelagibacter ubique. The ubiquity of MPnS-containing microbes supports the proposal that methylphosphonate is a source of methane in the upper, aerobic ocean, where phosphorus-starved microbes catabolize methylphosphonate for its phosphorus.


  • Organizational Affiliation

    Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylphosphonate synthase
A, B, C, D, E
A, B, C, D, E, F, G, H
457Nitrosopumilus maritimus SCM1Mutation(s): 0 
Gene Names: mpnSNmar_0155
EC: 1.13.11.73
UniProt
Find proteins for A9A1T2 (Nitrosopumilus maritimus (strain SCM1))
Explore A9A1T2 
Go to UniProtKB:  A9A1T2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9A1T2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2HE (Subject of Investigation/LOI)
Query on 2HE

Download Ideal Coordinates CCD File 
BA [auth G]
EA [auth H]
J [auth A]
M [auth B]
P [auth C]
BA [auth G],
EA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
(2-hydroxyethyl)phosphonic acid
C2 H7 O4 P
SEHJHHHUIGULEI-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
I [auth A]
K [auth B]
L [auth B]
AA [auth G],
DA [auth H],
I [auth A],
K [auth B],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
CA [auth G]
N [auth B]
Q [auth C]
T [auth D]
W [auth E]
CA [auth G],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.85α = 90
b = 351.25β = 103.36
c = 76.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States1S10RR029205-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States3P41GM103403-15S1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM008313-29

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations