6B9R

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

PDB DOI: https://doi.org/10.2210/pdb6B9R/pdb

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

PubMed: 29217579 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 199.55 kDa
Atom Count: 15,644
Modelled Residue Count: 1,772
Deposited Residue Count: 1,800
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyethylphosphonate dioxygenase	A, B, C, D	450	Streptomyces albus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2HE (Subject of Investigation/LOI) Query on 2HE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D]	F [auth A], I [auth B], M [auth C], Q [auth D]	(2-hydroxyethyl)phosphonic acid C₂ H₇ O₄ P SEHJHHHUIGULEI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D]	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		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D]	E [auth A], H [auth B], L [auth C], P [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D]

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 = 89.238	α = 90
b = 100.707	β = 92.27
c = 99.088	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
SHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Born, D.A.

Drennan, C.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	1S10RR029205-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	3P41GM103403-15S1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5T32GM008313-29

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

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Help and Resources

6B9R

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

Structural basis for methylphosphonate biosynthesis.

Entity ID: 1

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)