8RP2 | pdb_00008rp2

Aminodeoxychorismate synthase complex from Escherichia coli, with EDTA added


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.201 (DCC) 

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

Activity Regulation of a Glutamine Amidotransferase Bienzyme Complex by Substrate-Induced Subunit Interface Expansion.

Funke, F.J.Schlee, S.Bento, I.Bourenkov, G.Sterner, R.Wilmanns, M.

(2025) ACS Catal 15: 4359-4373

  • DOI: https://doi.org/10.1021/acscatal.4c07438
  • Primary Citation of Related Structures:  
    8RP0, 8RP1, 8RP2, 8RP6, 8RP7

  • PubMed Abstract: 

    Glutamine amidotransferases are multienzyme machineries in which reactive ammonia is generated by a glutaminase and then transferred through a sequestered protein tunnel to a synthase active site for incorporation into diverse metabolites. To avoid wasteful metabolite consumption, there is a requirement for synchronized catalysis, but any generally applicable mechanistic insight is still lacking. As synthase activity depends on glutamine turnover, we investigated possible mechanisms controlling glutaminase catalysis using aminodeoxychorismate synthase involved in folate biosynthesis as a model. By analyzing this system in distinct states of catalysis, we found that incubation with glutamine leads to a subunit interface expansion by one-third of its original area. These changes completely enclose the glutaminase active site for sequestered catalysis and the subsequent transport of volatile ammonia to the synthase active site. In view of similar rearrangements in other glutamine amidotransferases, our observations may provide a general mechanism for the catalysis synchronization of this multienzyme family.


  • Organizational Affiliation

    Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg 93040, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminodeoxychorismate synthase component 2A [auth AAA],
B [auth BBB]
189Escherichia coliMutation(s): 0 
Gene Names: pabAb3360JW3323
EC: 2.6.1.85
UniProt
Find proteins for P00903 (Escherichia coli (strain K12))
Explore P00903 
Go to UniProtKB:  P00903
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00903
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aminodeoxychorismate synthase component 1C [auth CCC],
D [auth DDD]
454Escherichia coliMutation(s): 0 
Gene Names: pabBb1812JW1801
EC: 2.6.1.85
UniProt
Find proteins for P05041 (Escherichia coli (strain K12))
Explore P05041 
Go to UniProtKB:  P05041
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05041
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRP (Subject of Investigation/LOI)
Query on TRP

Download Ideal Coordinates CCD File 
H [auth CCC],
R [auth DDD]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
O [auth CCC],
Y [auth DDD]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth DDD],
F [auth AAA],
G [auth AAA],
Q [auth CCC]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
P [auth CCC],
Z [auth DDD]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth AAA]
J [auth CCC]
K [auth CCC]
L [auth CCC]
M [auth CCC]
E [auth AAA],
J [auth CCC],
K [auth CCC],
L [auth CCC],
M [auth CCC],
N [auth CCC],
U [auth DDD],
V [auth DDD],
W [auth DDD],
X [auth DDD]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth CCC],
S [auth DDD],
T [auth DDD]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.965α = 90
b = 109.446β = 90
c = 178.859γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union664726

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Database references