6B9R

Streptomyces albus HEPD with substrate 2-hydroxyethylphosphonate (2-HEP) and Fe(II) bound

  • Classification: OXIDOREDUCTASE
  • Organism(s): Streptomyces albus
  • 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: 1.80 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


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
Hydroxyethylphosphonate dioxygenase
A, B, C, D
450Streptomyces albusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • 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 
F [auth A],
I [auth B],
M [auth C],
Q [auth D]
(2-hydroxyethyl)phosphonic acid
C2 H7 O4 P
SEHJHHHUIGULEI-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
K [auth B]
N [auth C]
O [auth C]
G [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
P [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.238α = 90
b = 100.707β = 92.27
c = 99.088γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
SHARPphasing

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