4WUI

Crystal structure of TrpF from Jonesia denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-(5'-phosphoribosyl)anthranilate isomerase
A
207Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134)Mutation(s): 0 
Gene Names: trpF
EC: 5.3.1.24
Find proteins for C7R2I5 (Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134))
Go to UniProtKB:  C7R2I5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 49.423α = 90.00
b = 64.289β = 90.00
c = 66.414γ = 90.00
Software Package:
Software NamePurpose
SBC-Collectdata collection
SHARPphasing
HKL-3000phasing
PHENIXrefinement
ARPmodel building
HKL-3000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM094585

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Refinement description
  • Version 1.2: 2015-02-04
    Type: Derived calculations
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-08
    Type: Database references