3G7D

Native PhpD with Cadmium Atoms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis.

Cicchillo, R.M.Zhang, H.Blodgett, J.A.Whitteck, J.T.Li, G.Nair, S.K.van der Donk, W.A.Metcalf, W.W.

(2009) Nature 459: 871-874

  • DOI: 10.1038/nature07972

  • PubMed Abstract: 
  • Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture. One such compound, phosphinothricin tripeptide, contains the unusual amino acid phosphinothricin attached to two alanine residues. Synthetic ph ...

    Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture. One such compound, phosphinothricin tripeptide, contains the unusual amino acid phosphinothricin attached to two alanine residues. Synthetic phosphinothricin (glufosinate) is a component of two top-selling herbicides (Basta and Liberty), and is widely used with resistant transgenic crops including corn, cotton and canola. Recent genetic and biochemical studies showed that during phosphinothricin tripeptide biosynthesis 2-hydroxyethylphosphonate (HEP) is converted to hydroxymethylphosphonate (HMP). Here we report the in vitro reconstitution of this unprecedented C(sp(3))-C(sp(3)) bond cleavage reaction and X-ray crystal structures of the enzyme. The protein is a mononuclear non-haem iron(ii)-dependent dioxygenase that converts HEP to HMP and formate. In contrast to most other members of this family, the oxidative consumption of HEP does not require additional cofactors or the input of exogenous electrons. The current study expands the scope of reactions catalysed by the 2-His-1-carboxylate mononuclear non-haem iron family of enzymes.


    Organizational Affiliation

    Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PhpD
A
443Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494)Mutation(s): 0 
Gene Names: hepD (phpD)
EC: 1.13.11.72
Find proteins for Q5IW40 (Streptomyces viridochromogenes (strain DSM 40736 / JCM 4977 / BCRC 1201 / Tue 494))
Go to UniProtKB:  Q5IW40
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 85.198α = 90.00
b = 95.736β = 90.00
c = 102.163γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
SHARPphasing
HKL-2000data reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-02-09 
  • Released Date: 2009-06-09 
  • Deposition Author(s): Nair, S.K.

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-28
    Type: Database references