Crystal Structure of 5-Enolpyruvulshikimate-3-phosphate Synthase from a Psychrophilic Bacterium, Colwellia psychrerythraea

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 

Starting Model: experimental
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Crystal structure of 5-enolpyruvylshikimate-3-phosphate synthase from a psychrophilic bacterium, Colwellia psychrerythraea 34H.

Lee, J.H.Choi, J.M.Kim, H.J.

(2017) Biochem Biophys Res Commun 492: 500-506

  • DOI: https://doi.org/10.1016/j.bbrc.2017.08.063
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    To survive at low temperatures, psychrophiles seem to produce cold-adapted enzymes with a high flexibility around active sites for high catalytic efficiency. To gain insights into the cold-adaptation of psychrophilic enzymes in atomic detail, we determined the crystal structure of 5-enolpyruvylshikimate-3-phosphate synthase (CpsEPSPS) from Colwellia psychrerythraea, a psychrophilic bacterium. EPSPS is the primary target for the broad-spectrum herbicide, glyphosate, and a promising target for the development of antimicrobial and antiparasitic agents since it is absent in animals. The crystal structure of unliganded, open CpsEPSPS was determined at 2.2 Å resolution in space group P2 1 with two protomers per asymmetric unit. Superposition of separate domain I and II of CpsEPSPS structure with those of Escherichia coli EPSPS (EcoEPSPS) structure showed relatively small differences of RMSD values of 0.423 Å and 0.693 Å for domains I and II, respectively, implying the residues in ligand binding and catalysis of cold-adapted CpsEPSPS showed no significant flexibility. This result is conflicting to other cases of cold-adapted proteins. We also observed that hydrogen-bond forming residues in the surface of EcoEPSPS was mutated to non- or lesser hydrogen-bond forming one in CpsEPSPS, which makes the protein surface softer and eventually makes the protein more active at low temperature. In addition, domain rotation angle between open and closed states of CpsEPSPS was smaller than those of any EPSPSs whose structures are known. The restriction of the domain closure, which reduces the entropy cost of ligand binding and catalysis, may be a novel molecular adaptations of cold-adapted enzymes.

  • Organizational Affiliation

    Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-phosphoshikimate 1-carboxyvinyltransferase
A, B
446Colwellia psychrerythraea 34HMutation(s): 0 
Gene Names: aroACPS_2333
Find proteins for Q482G5 (Colwellia psychrerythraea (strain 34H / ATCC BAA-681))
Explore Q482G5 
Go to UniProtKB:  Q482G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ482G5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.798α = 90
b = 80.027β = 96.46
c = 82.271γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling
MOLREPmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description