5XZ8

Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate (the ATP analog) and fructose-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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This is version 1.2 of the entry. See complete history


Literature

Structural Insights into the Regulation of Staphylococcus aureus Phosphofructokinase by Tetramer-Dimer Conversion.

Tian, T.Wang, C.L.Wu, M.H.Zhang, X.Zang, J.Y.

(2018) Biochemistry 57: 4252-4262

  • DOI: 10.1021/acs.biochem.8b00028
  • Primary Citation of Related Structures:  
    5XOE, 5XZ6, 5XZ7, 5XZ8, 5XZ9, 5XZA

  • PubMed Abstract: 
  • Most reported bacterial phosphofructokinases (Pfks) are tetramers that exhibit activity allosterically regulated via conformational changes between the R and T states. We report that the Pfk from Staphylococcus aureus NCTC 8325 ( SaPfk) exists as both an active tetramer and an inactive dimer in solution ...

    Most reported bacterial phosphofructokinases (Pfks) are tetramers that exhibit activity allosterically regulated via conformational changes between the R and T states. We report that the Pfk from Staphylococcus aureus NCTC 8325 ( SaPfk) exists as both an active tetramer and an inactive dimer in solution. Multiple effectors, including pH, ADP, ATP, and adenylyl-imidodiphosphate (AMP-PNP), cause equilibrium shifts from the tetramer to dimer, whereas the substrate F6P stabilizes SaPfk tetrameric assembly. Crystal structures of SaPfk in complex with different ligands and biochemical analysis reveal that the flexibility of the Gly150-Leu151 motif in helix α7 plays a role in tetramer-dimer conversion. Thus, we propose a molecular mechanism for allosteric regulation of bacterial Pfk via conversion between the tetramer and dimer in addition to the well-characterized R-state/T-state mechanism.


    Organizational Affiliation

    Key Laboratory of Structural Biology , Chinese Academy of Sciences , Hefei , Anhui 230026 , China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent 6-phosphofructokinaseA330Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: pfkASAOUHSC_01807
EC: 2.7.1.11
UniProt
Find proteins for Q2FXM8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXM8 
Go to UniProtKB:  Q2FXM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FXM8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
G [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
F6P
Query on F6P

Download Ideal Coordinates CCD File 
B [auth A]6-O-phosphono-beta-D-fructofuranose
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.36α = 90
b = 79.83β = 90
c = 120.39γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary