6YVB

Arabidopsis aspartate transcarbamoylase complex with carbamoyl phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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: https://doi.org/10.1038/s41467-021-21165-9
  • Primary Citation of Related Structures:  
    6YPO, 6YS6, 6YSP, 6YVB, 6YW9, 6YWJ, 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. 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

    Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Strasse, D-67663, Kaiserslautern, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PYRB
A, B, C, D, E
A, B, C, D, E, F
332Arabidopsis thalianaMutation(s): 0 
Gene Names: AXX17_At3g21670
EC: 2.1.3.2
UniProt
Find proteins for P49077 (Arabidopsis thaliana)
Explore P49077 
Go to UniProtKB:  P49077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49077
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CP (Subject of Investigation/LOI)
Query on CP

Download Ideal Coordinates CCD File 
BA [auth D]
FA [auth E]
G [auth A]
JA [auth F]
O [auth B]
BA [auth D],
FA [auth E],
G [auth A],
JA [auth F],
O [auth B],
V [auth C]
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
C H4 N O5 P
FFQKYPRQEYGKAF-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth D]
EA [auth E]
GA [auth E]
H [auth A]
HA [auth E]
CA [auth D],
EA [auth E],
GA [auth E],
H [auth A],
HA [auth E],
I [auth A],
J [auth A],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
NA [auth F],
P [auth B],
Q [auth B],
R [auth B],
T [auth B],
W [auth C],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth C]
DA [auth D]
IA [auth E]
M [auth A]
MA [auth F]
AA [auth C],
DA [auth D],
IA [auth E],
M [auth A],
MA [auth F],
N [auth A],
S [auth B],
U [auth B],
Y [auth C],
Z [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.268α = 90
b = 109.481β = 90
c = 212.042γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata 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
German Research Foundation (DFG)GermanyMo 1032/4-1)
German Research Foundation (DFG)GermanyIRTG 1830

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description