6YPO

Arabidopsis aspartate transcarbamoylase bound to UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 

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Ligand Structure Quality Assessment 


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Literature

Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase.

Bellin, L.Del Cano-Ochoa, F.Velazquez-Campoy, A.Mohlmann, T.Ramon-Maiques, S.

(2021) Nat Commun 12: 947-947

  • DOI: 10.1038/s41467-021-21165-9
  • Primary Citation of Related Structures:  
    6YPO, 6YS6, 6YSP, 6YVB, 6YWJ, 6YW9, 6YY1

  • PubMed Abstract: 
  • Aspartate transcarbamoylase (ATC), an essential enzyme for de novo pyrimidine biosynthesis, is uniquely regulated in plants by feedback inhibition of uridine 5-monophosphate (UMP). Despite its importance in plant growth, the structure of this UMP-controlled ATC and the regulatory mechanism remain unknown ...

    Aspartate transcarbamoylase (ATC), an essential enzyme for de novo pyrimidine biosynthesis, is uniquely regulated in plants by feedback inhibition of uridine 5-monophosphate (UMP). Despite its importance in plant growth, the structure of this UMP-controlled ATC and the regulatory mechanism remain unknown. Here, we report the crystal structures of Arabidopsis ATC trimer free and bound to UMP, complexed to a transition-state analog or bearing a mutation that turns the enzyme insensitive to UMP. We found that UMP binds and blocks the ATC active site, directly competing with the binding of the substrates. We also prove that UMP recognition relies on a loop exclusively conserved in plants that is also responsible for the sequential firing of the active sites. In this work, we describe unique regulatory and catalytic properties of plant ATCs that could be exploited to modulate de novo pyrimidine synthesis and plant growth.


    Organizational Affiliation

    Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)- Instituto de Salud Carlos III, Valencia, Spain. sramon@ibv.csic.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYRBA, B332Arabidopsis thalianaMutation(s): 0 
Gene Names: AXX17_At3g21670PYRBAt3g20330MQC12.7
EC: 2.1.3.2
UniProt
Find proteins for P49077 (Arabidopsis thaliana)
Explore P49077 
Go to UniProtKB:  P49077
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.541α = 90
b = 104.541β = 90
c = 127.79γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
EDNAdata collection
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2016-80570-R
Spanish Ministry of Science, Innovation, and UniversitiesSpainRTI2018-098084-B-100

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release