4U28

Crystal structure of apo Phosphoribosyl isomerase A from Streptomyces sviceus ATCC 29083


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Co-occurrence of analogous enzymes determines evolution of a novel ( beta alpha )8-isomerase sub-family after non-conserved mutations in flexible loop.

Verduzco-Castro, E.A.Michalska, K.Endres, M.Juarez-Vazquez, A.L.Noda-Garcia, L.Chang, C.Henry, C.S.Babnigg, G.Joachimiak, A.Barona-Gomez, F.

(2016) Biochem. J. 473: 1141-1152

  • DOI: 10.1042/BJ20151271
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We investigate the evolution of co-occurring analogous enzymes involved in L-tryptophan and L-histidine biosynthesis in Actinobacteria Phylogenetic analysis of trpF homologues, a missing gene in certain clades of this lineage whose absence is complem ...

    We investigate the evolution of co-occurring analogous enzymes involved in L-tryptophan and L-histidine biosynthesis in Actinobacteria Phylogenetic analysis of trpF homologues, a missing gene in certain clades of this lineage whose absence is complemented by a dual-substrate HisA homologue, termed PriA, found that they fall into three categories: (i) trpF-1, an L-tryptophan biosynthetic gene horizontally acquired by certain Corynebacterium species; (ii) trpF-2, a paralogue known to be involved in synthesizing a pyrrolopyrrole moiety and (iii) trpF-3, a variable non-conserved orthologue of trpF-1 We previously investigated the effect of trpF-1 upon the evolution of PriA substrate specificity, but nothing is known about the relationship between trpF-3 and priA After in vitro steady-state enzyme kinetics we found that trpF-3 encodes a phosphoribosyl anthranilate isomerase. However, mutation of this gene in Streptomyces sviceus did not lead to auxothrophy, as expected from the biosynthetic role of trpF-1 Biochemical characterization of a dozen co-occurring TrpF-2 or TrpF-3, with PriA homologues, explained the prototrophic phenotype, and unveiled an enzyme activity trade-off between TrpF and PriA. X-ray structural analysis suggests that the function of these PriA homologues is mediated by non-conserved mutations in the flexible L5 loop, which may be responsible for different substrate affinities. Thus, the PriA homologues that co-occur with TrpF-3 represent a novel enzyme family, termed PriB, which evolved in response to PRA isomerase activity. The characterization of co-occurring enzymes provides insights into the influence of functional redundancy on the evolution of enzyme function, which could be useful for enzyme functional annotation.


    Organizational Affiliation

    Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, CP36821, México fbarona@langebio.cinvestav.mx.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A. Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A.,Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A. Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A. Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, U.S.A.,Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, CP36821, México.,Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois 60439, U.S.A.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoribosyl isomerase A
A
245Streptomyces sviceus ATCC 29083Mutation(s): 0 
Gene Names: priA (hisA)
Find proteins for B5I4P8 (Streptomyces sviceus ATCC 29083)
Go to UniProtKB:  B5I4P8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.127 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.111α = 90.00
b = 69.111β = 90.00
c = 175.036γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Derived calculations
  • Version 1.2: 2015-02-11
    Type: Other
  • Version 1.3: 2017-11-08
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy