4XB6

Structure of the E. coli C-P lyase core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into the bacterial carbon-phosphorus lyase machinery.

Seweryn, P.Van, L.B.Kjeldgaard, M.Russo, C.J.Passmore, L.A.Hove-Jensen, B.Jochimsen, B.Brodersen, D.E.

(2015) Nature 525: 68-72

  • DOI: 10.1038/nature14683

  • PubMed Abstract: 
  • Phosphorus is required for all life and microorganisms can extract it from their environment through several metabolic pathways. When phosphate is in limited supply, some bacteria are able to use phosphonate compounds, which require specialized enzym ...

    Phosphorus is required for all life and microorganisms can extract it from their environment through several metabolic pathways. When phosphate is in limited supply, some bacteria are able to use phosphonate compounds, which require specialized enzymatic machinery to break the stable carbon-phosphorus (C-P) bond. Despite its importance, the details of how this machinery catabolizes phosphonates remain unknown. Here we determine the crystal structure of the 240-kilodalton Escherichia coli C-P lyase core complex (PhnG-PhnH-PhnI-PhnJ; PhnGHIJ), and show that it is a two-fold symmetric hetero-octamer comprising an intertwined network of subunits with unexpected self-homologies. It contains two potential active sites that probably couple phosphonate compounds to ATP and subsequently hydrolyse the C-P bond. We map the binding site of PhnK on the complex using electron microscopy, and show that it binds to a conserved insertion domain of PhnJ. Our results provide a structural basis for understanding microbial phosphonate breakdown.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG
A, E
150Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: phnG
EC: 2.7.8.37
Find proteins for P16685 (Escherichia coli (strain K12))
Go to UniProtKB:  P16685
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH
B, F
194Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: phnH
EC: 2.7.8.37
Find proteins for P16686 (Escherichia coli (strain K12))
Go to UniProtKB:  P16686
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI
C, G
354Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: phnI
EC: 2.7.8.37
Find proteins for P16687 (Escherichia coli (strain K12))
Go to UniProtKB:  P16687
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase
D, H
281Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: phnJ
EC: 4.7.1.1
Find proteins for P16688 (Escherichia coli (strain K12))
Go to UniProtKB:  P16688
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C, D, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
C, D, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
B, F
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.510α = 90.00
b = 133.710β = 90.00
c = 176.740γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-12-16 
  • Released Date: 2015-08-19 
  • Deposition Author(s): Brodersen, D.E.

Funding OrganizationLocationGrant Number
Danish National Research FoundationDenmarkCentre for mRNP Biogenesis and Metabolism

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references
  • Version 1.2: 2015-09-09
    Type: Database references