6IHC

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) Y100A mutant in complex with holo-ACP from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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Literature

A back-door Phenylalanine coordinates the stepwise hexameric loading of acyl carrier protein by the fatty acid biosynthesis enzyme beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ).

Shen, S.Q.Hang, X.D.Zhuang, J.J.Zhang, L.Bi, H.K.Zhang, L.

(2019) Int J Biol Macromol 128: 5-11

  • DOI: https://doi.org/10.1016/j.ijbiomac.2019.01.094
  • Primary Citation of Related Structures:  
    6IHC

  • PubMed Abstract: 
  • The fatty acid biosynthesis pathway (FAS) was a fundamental procedure to generate a diversity of lipid components for cellular metabolism in bacteria, while the mechanism of substrate recognition remains unclear. The β-hydroxyacyl-acyl carrier protein dehydratase hexamer (FabZ) is an essential module in the elongation cycle of type-II FAS, catalyzing the dehydration of β-hydroxyacyl-lipid substrate carried by the holo form acyl carrier protein (holo-ACP) ...

    The fatty acid biosynthesis pathway (FAS) was a fundamental procedure to generate a diversity of lipid components for cellular metabolism in bacteria, while the mechanism of substrate recognition remains unclear. The β-hydroxyacyl-acyl carrier protein dehydratase hexamer (FabZ) is an essential module in the elongation cycle of type-II FAS, catalyzing the dehydration of β-hydroxyacyl-lipid substrate carried by the holo form acyl carrier protein (holo-ACP). We previously elucidated an alternating seesaw-like ACP loading manner within a FabZ dimer subunits, mediated by a front-door residue Tyrosine (Tyr100). Here, we demonstrated that a back-door residue Phenylalanine (Phe83) of FabZ regulates the stepwise hexameric loading of ACP. Our finding represents clues as to the dynamic ACP recognition and catalysis mechanism of dehydratase in fatty acid biosynthesis, and provides critical information for developing antimicrobials targeting the dehydratase module in fatty acid biosynthesis pathway.


    Organizational Affiliation

    Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Universities Collaborative Innovation Center for Translational Medicine, Shanghai, PR China. Electronic address: liangzhang2014@sjtu.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
A, B, C, D, E
A, B, C, D, E, F
153Helicobacter pyloriMutation(s): 0 
Gene Names: fabZAOD77_0202395BB395_03990BFR58_03630DD756_07280DD767_06730DDP42_00065EC592_05795EDA73_06725HPPMSS1_c00137
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
holo-form acyl carrier protein (holo-ACP)65Helicobacter pyloriMutation(s): 0 
UniProt
Find proteins for B6JLE2 (Helicobacter pylori (strain P12))
Explore B6JLE2 
Go to UniProtKB:  B6JLE2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6JLE2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PN7
Query on PN7

Download Ideal Coordinates CCD File 
K [auth G]N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-SECBINFHSA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
H [auth A],
I [auth C],
J [auth F]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 272.528α = 90
b = 76.9β = 99.23
c = 72.991γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21722802

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release