8JFN | pdb_00008jfn

Crystal structure of enoyl-ACP reductase FabI in complex with NAD+ and crotonyl-ACP from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.235 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.183 (Depositor) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

The Molecular Basis of Catalysis by SDR Family Members Ketoacyl-ACP Reductase FabG and Enoyl-ACP Reductase FabI in Type-II Fatty Acid Biosynthesis.

Zhou, J.Zhang, L.Wang, Y.Song, W.Huang, Y.Mu, Y.Schmitz, W.Zhang, S.Y.Lin, H.Chen, H.Z.Ye, F.Zhang, L.

(2023) Angew Chem Int Ed Engl 62: e202313109-e202313109

  • DOI: https://doi.org/10.1002/anie.202313109
  • Primary Citation Related Structures: 
    8JF9, 8JFA, 8JFG, 8JFH, 8JFI, 8JFJ, 8JFM, 8JFN

  • PubMed Abstract: 

    The short-chain dehydrogenase/reductase (SDR) superfamily members acyl-ACP reductases FabG and FabI are indispensable core enzymatic modules and catalytic orientation controllers in type-II fatty acid biosynthesis. Herein, we report their distinct substrate allosteric recognition and enantioselective reduction mechanisms. FabG achieves allosteric regulation of ACP and NADPH through ACP binding across two adjacent FabG monomers, while FabI follows an irreversible compulsory order of substrate binding in that NADH binding must precede that of ACP on a discrete FabI monomer. Moreover, FabG and FabI utilize a backdoor residue Phe187 or a "rheostat" α8 helix for acyl chain length selection, and their corresponding triad residues Ser142 or Tyr145 recognize the keto- or enoyl-acyl substrates, respectively, facilitating initiation of nucleophilic attack by NAD(P)H. The other two triad residues (Tyr and Lys) mediate subsequent proton transfer and (R)-3-hydroxyacyl- or saturated acyl-ACP production.


  • Organizational Affiliation
    • Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.

Macromolecule Content 

  • Total Structure Weight: 39.58 kDa 
  • Atom Count: 2,848 
  • Modeled Residue Count: 350 
  • Deposited Residue Count: 353 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]273Helicobacter pyloriMutation(s): 0 
Gene Names: fabI
EC: 1.3.1.9
UniProt
Find proteins for A0A086RSH0 (Helicobacter pylori)
Explore A0A086RSH0 
Go to UniProtKB:  A0A086RSH0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A086RSH0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl carrier protein80Helicobacter pyloriMutation(s): 0 
Gene Names: acpP
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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
C [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PSR
(Subject of Investigation/LOI)

Query on PSR



Download:Ideal Coordinates CCD File
D [auth B]THIOBUTYRIC ACID S-{2-[3-(2-HYDROXY-3,3-DIMETHYL-4-PHOSPHONOOXY-BUTYRYLAMINO)-PROPIONYLAMINO]-ETHYL} ESTER
C15 H29 N2 O8 P S
PZIQDUSGQUZEBS-CYBMUJFWSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.235 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.183 (Depositor) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.272α = 90
b = 101.816β = 90
c = 126.329γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
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 China (NSFC)China22077081

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary