4U7W

The crystal structure of the terminal R domain from the myxalamid PKS-NRPS biosynthetic pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.899 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols.

Barajas, J.F.Phelan, R.M.Schaub, A.J.Kliewer, J.T.Kelly, P.J.Jackson, D.R.Luo, R.Keasling, J.D.Tsai, S.C.

(2015) Chem.Biol. 22: 1018-1029

  • DOI: 10.1016/j.chembiol.2015.06.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The terminal reductase (R) domain from the non-ribosomal peptide synthetase (NRPS) module MxaA in Stigmatella aurantiaca Sga15 catalyzes a non-processive four-electron reduction to produce the myxalamide family of secondary metabolites. Despite wides ...

    The terminal reductase (R) domain from the non-ribosomal peptide synthetase (NRPS) module MxaA in Stigmatella aurantiaca Sga15 catalyzes a non-processive four-electron reduction to produce the myxalamide family of secondary metabolites. Despite widespread use in nature, a lack of structural and mechanistic information concerning reductive release from polyketide synthase (PKS) and NRPS assembly lines principally limits our ability to redesign R domains with altered or improved activity. Here we report crystal structures for MxaA R, both in the absence and, for the first time, in the presence of the NADPH cofactor. Molecular dynamics simulations were employed to provide a deeper understanding of this domain and further identify residues critical for structural integrity, substrate binding, and catalysis. Aggregate computational and structural findings provided a basis for mechanistic investigations and, in the process, delivered a rationally altered variant with improved activity toward highly reduced substrates.


    Organizational Affiliation

    Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA.,Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.,Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: keasling@berkeley.edu.,Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA. Electronic address: sctsai@uci.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MxaA
A, B
420Stigmatella aurantiacaMutation(s): 0 
Gene Names: mxaA
Find proteins for Q93TX2 (Stigmatella aurantiaca)
Go to UniProtKB:  Q93TX2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NDPKd: 45000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.899 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.106α = 90.00
b = 159.050β = 106.14
c = 51.184γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States5R01GM100305-03
National Institutes of Health/National Institute of General Medical SciencesUnited States5F31GM100738-02

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations