6C9U

Crystal structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase in complex with antibody fragment (Fab)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-Function Analysis of the Extended Conformation of a Polyketide Synthase Module.

Li, X.Sevillano, N.La Greca, F.Deis, L.Liu, Y.C.Deller, M.C.Mathews, I.I.Matsui, T.Cane, D.E.Craik, C.S.Khosla, C.

(2018) J. Am. Chem. Soc. 140: 6518-6521

  • DOI: 10.1021/jacs.8b02100

  • PubMed Abstract: 
  • Catalytic modules of assembly-line polyketide synthases (PKSs) have previously been observed in two very different conformations-an "extended" architecture and an "arch-shaped" architecture-although the catalytic relevance of neither has been directl ...

    Catalytic modules of assembly-line polyketide synthases (PKSs) have previously been observed in two very different conformations-an "extended" architecture and an "arch-shaped" architecture-although the catalytic relevance of neither has been directly established. By the use of a fully human naïve antigen-binding fragment (F ab ) library, a high-affinity antibody was identified that bound to the extended conformation of a PKS module, as verified by X-ray crystallography and tandem size-exclusion chromatography-small-angle X-ray scattering (SEC-SAXS). Kinetic analysis proved that this antibody-stabilized module conformation was fully competent for catalysis of intermodular polyketide chain translocation as well as intramodular polyketide chain elongation and functional group modification of a growing polyketide chain. Thus, the extended conformation of a PKS module is fully competent for all of its essential catalytic functions.


    Organizational Affiliation

    Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia.,Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018, Zaragoza, Spain.,Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (J.M.B., M.L.W., A.M.R., A.A.P.) and School of Biological Sciences, University of Auckland, Auckland, New Zealand (D.L.H.) augen-pioszak@ouhsc.edu.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (J.M.B., M.L.W., A.M.R., A.A.P.) and School of Biological Sciences, University of Auckland, Auckland, New Zealand (D.L.H.).,Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009, Bilbao, Spain.,IGF, Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France.,Department of Pharmaceutical Chemistry, University of Debrecen, 4032, Debrecen, Hungary.,Dept. of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.,CRBM, "Equipe Labellisée Ligue Contre le Cancer", Univ Montpellier, CNRS, 34000 Montpellier, France. Electronic address: serge.roche@crbm.cnrs.fr.,CBS, Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France. Electronic address: gilles.labesse@cbs.cnrs.fr.,School of Life Sciences, University of Dundee, Dundee, United Kingdom.,CBS, Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , United States.,UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.,Fundación ARAID, 50018, Zaragoza, Spain.,Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, United Kingdom.,Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain.,University of Chinese Academy of Sciences, Beijing, 101408, China.,Department of Chemistry , Box H, Brown University , Providence , Rhode Island 02912-9108 , United States.,CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain.,CRBM, "Equipe Labellisée Ligue Contre le Cancer", Univ Montpellier, CNRS, 34000 Montpellier, France.,Department of Pharmaceutical Chemistry , University of California San Francisco , San Francisco , California 94158 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-deoxyerythronolide-B synthase EryA2, modules 3 and 4
A
941Saccharopolyspora erythraeaMutation(s): 0 
Gene Names: eryA
EC: 2.3.1.94
Find proteins for Q03132 (Saccharopolyspora erythraea)
Go to UniProtKB:  Q03132
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Light chain of Fab 1B2
L
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of Fab 1B2
H
249N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.768α = 90.00
b = 139.684β = 97.05
c = 102.580γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

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 StatesGM087934

Revision History 

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-05-30
    Type: Data collection, Database references
  • Version 1.2: 2018-06-06
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection