8HX8

Crystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae co-crystallized with chorismate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

Starting Model: other
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Literature

Structural basis for the allosteric pathway of 4-amino-4-deoxychorismate synthase.

Nakamichi, Y.Kobayashi, J.Toyoda, K.Suda, M.Hiraga, K.Inui, M.Watanabe, M.

(2023) Acta Crystallogr D Struct Biol 79: 895-908

  • DOI: https://doi.org/10.1107/S2059798323006320
  • Primary Citation of Related Structures:  
    8HX6, 8HX7, 8HX8, 8HX9

  • PubMed Abstract: 

    4-Amino-4-deoxychorismate synthase (ADCS), a chorismate-utilizing enzyme, is composed of two subunits: PabA and PabB. PabA is a glutamine amidotransferase that hydrolyzes glutamine into glutamate and ammonia. PabB is an aminodeoxychorismate synthase that converts chorismate to 4-amino-4-deoxychorismate (ADC) using the ammonia produced by PabA. ADCS functions under allosteric regulation between PabA and PabB. However, the allosteric mechanism remains unresolved because the structure of the PabA-PabB complex has not been determined. Here, the crystal structure and characterization of PapA from Streptomyces venezuelae (SvPapA), a bifunctional enzyme comprising the PabA and PabB domains, is reported. SvPapA forms a unique dimer in which PabA and PabB domains from different monomers complement each other and form an active structure. The chorismate-bound structure revealed that recognition of the C1 carboxyl group by Thr501 and Gly502 of the 498-PIKTG-502 motif in the PabB domain is essential for the catalytic Lys500 to reach the C2 atom, a reaction-initiation site. SvPapA demonstrated ADCS activity in the presence of Mg 2+ when glutamate or NH + 4 was used as the amino donor. The crystal structure indicated that the Mg 2+ -binding position changed depending on the binding of chorismate. In addition, significant structural changes were observed in the PabA domain depending on the presence or absence of chorismate. This study provides insights into the structural factors that are involved in the allosteric regulation of ADCS.


  • Organizational Affiliation

    Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-amino-4-deoxychorismate synthase
A, B
702Streptomyces venezuelaeMutation(s): 0 
Gene Names: papA
EC: 2.6.1.85
UniProt
Find proteins for F2RB79 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745))
Go to UniProtKB:  F2RB79
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.334α = 90
b = 172.848β = 90
c = 161.054γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentJapan1091195

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection