5XD7

Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Crystal structure analysis of 3,6-anhydro-l-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily.

Lee, S.Kim, K.H.Kim, H.-Y.Choi, I.-G.

(2017) Biochem Biophys Res Commun 491: 217-222

  • DOI: https://doi.org/10.1016/j.bbrc.2017.07.080
  • Primary Citation of Related Structures:  
    5XD7, 5XD8, 5XD9

  • PubMed Abstract: 

    3,6-Anydro-l-galatonate cycloisomerase (ACI) catalyzes the cycloisomerization of a 3,6-anhydro-l-galactonic acid known as a novel metabolite in agarolytic bacteria. Here, we present 3-D structures of ACI from Vibrio sp. strain EJY3 (VejACI) in native and mutant forms at 2.2 Å and 2.6 Å resolutions, respectively. The enzyme belongs to the mandelate racemase subgroup of the enolase superfamily catalyzing common β-elimination reactions by α-carbon deprotonation of substrates. The structure of VejACI revealed a notable 20s loop region in the capping domain, which can be a highly conserved structural motif in ACI homologs of agar metabolism. By comparing mutant (mVejAC/H300 N) and native VejACI structures, we identified a conformational change of Ile142 in VejACI that causes spatial expansion in the binding pocket. These observations imply that Ile142 and the 20s loop play important roles in enzymatic reactivity and substrate specificity. The structural phylogenetic analysis of the enolase superfamily including ACIs revealed sequential, structural, and functional relationships related to the emergence of novel substrate specificity.


  • Organizational Affiliation

    Department of Biotechnology, Korea University Graduate School, 5 Anam-ro, Seoungbuk-gu, Seoul, 02841, South Korea; Protein Structure Group, Korea Basic Science Institute, Ochang, Chungbuk, 28119, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3,6-anhydro-alpha-L-galactonate cycloisomerase368Vibrio sp. EJY3Mutation(s): 0 
Gene Names: VejaciVEJY3_09370
EC: 5.5.1.25
UniProt
Find proteins for H2IFX0 (Vibrio sp. (strain EJY3))
Explore H2IFX0 
Go to UniProtKB:  H2IFX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2IFX0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.336α = 90
b = 87.336β = 90
c = 143.069γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Advisory, Data collection, Database references, Refinement description