5XZ9 | pdb_00005xz9

Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate, the ATP analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.248 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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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: https://doi.org/10.1021/acs.biochem.8b00028
  • Primary Citation 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. 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
    • Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China.

Macromolecule Content 

  • Total Structure Weight: 36.55 kDa 
  • Atom Count: 2,538 
  • Modeled Residue Count: 321 
  • Deposited Residue Count: 330 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent 6-phosphofructokinase330Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: pfkASAOUHSC_01807
EC: 2.7.1.11
UniProt
Find proteins for P99165 (Staphylococcus aureus (strain N315))
Explore P99165 
Go to UniProtKB:  P99165
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP99165
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.248 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.746α = 90
b = 36.79β = 123.82
c = 89.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2023-11-22
    Changes: Advisory, Data collection, Database references, Refinement description