4ZJB

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) in complex with holo-ACP from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of FabZ-ACP complex reveals a dynamic seesaw-like catalytic mechanism of dehydratase in fatty acid biosynthesis.

Zhang, L.Xiao, J.Xu, J.Fu, T.Cao, Z.Zhu, L.Chen, H.Z.Shen, X.Jiang, H.Zhang, L.

(2016) Cell Res 26: 1330-1344

  • DOI: https://doi.org/10.1038/cr.2016.136
  • Primary Citation of Related Structures:  
    4ZJB

  • PubMed Abstract: 

    Fatty acid biosynthesis (FAS) is a vital process in cells. Fatty acids are essential for cell assembly and cellular metabolism. Abnormal FAS directly correlates with cell growth delay and human diseases, such as metabolic syndromes and various cancers. The FAS system utilizes an acyl carrier protein (ACP) as a transporter to stabilize and shuttle the growing fatty acid chain throughout enzymatic modules for stepwise catalysis. Studying the interactions between enzymatic modules and ACP is, therefore, critical for understanding the biological function of the FAS system. However, the information remains unclear due to the high flexibility of ACP and its weak interaction with enzymatic modules. We present here a 2.55 Å crystal structure of type II FAS dehydratase FabZ in complex with holo-ACP, which exhibits a highly symmetrical FabZ hexamer-ACP 3 stoichiometry with each ACP binding to a FabZ dimer subunit. Further structural analysis, together with biophysical and computational results, reveals a novel dynamic seesaw-like ACP binding and catalysis mechanism for the dehydratase module in the FAS system, which is regulated by a critical gatekeeper residue (Tyr100 in FabZ) that manipulates the movements of the β-sheet layer. These findings improve the general understanding of the dehydration process in the FAS system and will potentially facilitate drug and therapeutic design for diseases associated with abnormalities in FAS.


  • Organizational Affiliation

    Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
A, B
171Helicobacter pyloriMutation(s): 0 
Gene Names: fabZ
EC: 4.2.1.59
UniProt
Find proteins for Q5G940 (Helicobacter pylori)
Explore Q5G940 
Go to UniProtKB:  Q5G940
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5G940
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinC [auth G]86Helicobacter pyloriMutation(s): 0 
Gene Names: acpPEG63_02640HPY173_03440HPY1786_00110HPY1846_06495HPY207_02635HPY228_03880HPY499_02145JM68_05695
UniProt
Find proteins for Q5EDC8 (Helicobacter pylori)
Explore Q5EDC8 
Go to UniProtKB:  Q5EDC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EDC8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.705α = 90
b = 127.705β = 90
c = 127.705γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data processing
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.2: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description