6N3P

Crosslinked AcpP=FabZ complex from E. coli Type II FAS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and dynamical rationale for fatty acid unsaturation inEscherichia coli.

Dodge, G.J.Patel, A.Jaremko, K.L.McCammon, J.A.Smith, J.L.Burkart, M.D.

(2019) Proc. Natl. Acad. Sci. U.S.A. 116: 6775-6783

  • DOI: 10.1073/pnas.1818686116

  • PubMed Abstract: 
  • Fatty acid biosynthesis in α- and γ-proteobacteria requires two functionally distinct dehydratases, FabA and FabZ. Here, mechanistic cross-linking facilitates the structural characterization of a stable hexameric complex of six <i>Escherichia coli < ...

    Fatty acid biosynthesis in α- and γ-proteobacteria requires two functionally distinct dehydratases, FabA and FabZ. Here, mechanistic cross-linking facilitates the structural characterization of a stable hexameric complex of six Escherichia coli FabZ dehydratase subunits with six AcpP acyl carrier proteins. The crystal structure sheds light on the divergent substrate selectivity of FabA and FabZ by revealing distinct architectures of the binding pocket. Molecular dynamics simulations demonstrate differential biasing of substrate orientations and conformations within the active sites of FabA and FabZ such that FabZ is preorganized to catalyze only dehydration, while FabA is primed for both dehydration and isomerization.


    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-2216; jmccammon@ucsd.edu JanetSmith@umich.edu mburkart@ucsd.edu.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0340; jmccammon@ucsd.edu JanetSmith@umich.edu mburkart@ucsd.edu.,Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0340.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0340.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-2216.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
A, B, C, D, E, F
154Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fabZ (sefA, yaeA)
EC: 4.2.1.59
Find proteins for P0A6Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6Q6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein
G, H, I, J, K, L
80Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acpP
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6A8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XLN
Query on XLN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N~3~-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-(3-{[(1Z)-pent-1-en-1-yl]sulfonyl}propyl)-beta-alaninamide
C17 H33 N2 O8 P S
FSMMECVJUFTNBW-FTXNUJCXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.136α = 90.00
b = 136.185β = 90.00
c = 152.272γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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 Diabetes and Digestive and Kidney DiseaseUnited StatesDK042303

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-03-27
    Type: Data collection, Database references
  • Version 1.2: 2019-04-10
    Type: Data collection, Database references