4X2R

Crystal structure of PriA from Actinomyces urogenitalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Evolution of substrate specificity in a retained enzyme driven by gene loss.

Juarez-Vazquez, A.L.Edirisinghe, J.N.Verduzco-Castro, E.A.Michalska, K.Wu, C.Noda-Garcia, L.Babnigg, G.Endres, M.Medina-Ruiz, S.Santoyo-Flores, J.Carrillo-Tripp, M.Ton-That, H.Joachimiak, A.Henry, C.S.Barona-Gomez, F.

(2017) Elife 6

  • DOI: 10.7554/eLife.22679
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomyce ...

    The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes.


    Organizational Affiliation

    Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomeraseA250Actinomyces urogenitalis DSM 15434Mutation(s): 0 
Gene Names: hisAHMPREF0058_1848
EC: 5.3.1.16
Find proteins for C0W7K4 (Actinomyces urogenitalis DSM 15434)
Explore C0W7K4 
Go to UniProtKB:  C0W7K4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CXS
Query on CXS

Download CCD File 
A
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 
  • Space Group: P 41
  • Diffraction Data DOI: 10.18430/M34X2R Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.02α = 90
b = 76.02β = 90
c = 43.179γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094585

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.2: 2017-11-08
    Changes: Database references
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence