Crystal structure of the r139n mutant of a bifunctional enzyme pria

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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Identification and Analysis of Residues Contained on Beta --> Alpha Loops of the Dual-Substrate (Betaalpha)(8) Phosphoribosyl Isomerase a (Pria) Specific for its Phosphoribosyl Anthranilate Isomerase Activity.

Noda-Garcia, L.Camacho-Zarco, A.R.Verdel-Aranda, K.Wright, H.Soberon, X.Fulop, V.Barona-Gomez, F.

(2010) Protein Sci 19: 535

  • DOI: https://doi.org/10.1002/pro.331
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A good model to experimentally explore evolutionary hypothesis related to enzyme function is the ancient-like dual-substrate (beta alpha)(8) phosphoribosyl isomerase A (PriA), which takes part in both histidine and tryptophan biosynthesis in Streptomyces coelicolor and related organisms. In this study, we determined the Michaelis-Menten enzyme kinetics for both isomerase activities in wild-type PriA from S. coelicolor and in selected single-residue monofunctional mutants, identified after Escherichia coli in vivo complementation experiments. Structural and functional analyses of a hitherto unnoticed residue contained on the functionally important beta --> alpha loop 5, namely, Arg(139), which was postulated on structural grounds to be important for the dual-substrate specificity of PriA, is presented for the first time. Indeed, enzyme kinetics analyses done on the mutant variants PriA_Ser(81)Thr and PriA_Arg(139)Asn showed that these residues, which are contained on beta --> alpha loops and in close proximity to the N-terminal phosphate-binding site, are essential solely for the phosphoribosyl anthranilate isomerase activity of PriA. Moreover, analysis of the X-ray crystallographic structure of PriA_Arg(139)Asn elucidated at 1.95 A herein strongly implicates the occurrence of conformational changes in this beta --> alpha loop as a major structural feature related to the evolution of the dual-substrate specificity of PriA. It is suggested that PriA has evolved by tuning a fine energetic balance that allows the sufficient degree of structural flexibility needed for accommodating two topologically dissimilar substrates--within a bifunctional and thus highly constrained active site--without compromising its structural stability.

  • Organizational Affiliation

    Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato, C.P. 36822, México.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHORIBOSYL ISOMERASE A240Streptomyces coelicolorMutation(s): 1 
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P16250 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore P16250 
Go to UniProtKB:  P16250
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16250
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.6α = 90
b = 63.6β = 90
c = 102.9γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description