2FZG

The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in Complex with Novel T State Inhibitors at 2.25 Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

T-state Inhibitors of E. coli Aspartate Transcarbamoylase that Prevent the Allosteric Transition.

Heng, S.Stieglitz, K.A.Eldo, J.Xia, J.Cardia, J.P.Kantrowitz, E.R.

(2006) Biochemistry 45: 10062-10071

  • DOI: 10.1021/bi0601095
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Escherichia coli aspartate transcarbamoylase (ATCase) catalyzes the committed step in pyrimidine nucleotide biosynthesis, the reaction between carbamoyl phosphate (CP) and l-aspartate to form N-carbamoyl-l-aspartate and inorganic phosphate. The enzym ...

    Escherichia coli aspartate transcarbamoylase (ATCase) catalyzes the committed step in pyrimidine nucleotide biosynthesis, the reaction between carbamoyl phosphate (CP) and l-aspartate to form N-carbamoyl-l-aspartate and inorganic phosphate. The enzyme exhibits homotropic cooperativity and is allosterically regulated. Upon binding l-aspartate in the presence of a saturating concentration of CP, the enzyme is converted from the low-activity low-affinity T state to the high-activity high-affinity R state. The potent inhibitor N-phosphonacetyl-l-aspartate (PALA), which combines the binding features of Asp and CP into one molecule, has been shown to induce the allosteric transition to the R state. In the presence of only CP, the enzyme is the T structure with the active site primed for the binding of aspartate. In a structure of the enzyme-CP complex (T(CP)), two CP molecules were observed in the active site approximately 7A apart, one with high occupancy and one with low occupancy. The high occupancy site corresponds to the position for CP observed in the structure of the enzyme with CP and the aspartate analogue succinate bound. The position of the second CP is in a unique site and does not overlap with the aspartate binding site. As a means to generate a new class of inhibitors for ATCase, the domain-open T state of the enzyme was targeted. We designed, synthesized, and characterized three inhibitors that were composed of two phosphonacetamide groups linked together. These two phosphonacetamide groups mimic the positions of the two CP molecules in the T(CP) structure. X-ray crystal structures of ATCase-inhibitor complexes revealed that each of these inhibitors bind to the T state of the enzyme and occupy the active site area. As opposed to the binding of Asp in the presence of CP or PALA, these inhibitors are unable to initiate the global T to R conformational change. Although the best of these T-state inhibitors only has a K(i) value in the micromolar range, the structural information with respect to their mode of binding provides important information for the design of second generation inhibitors that will have even higher affinity for the active site of the T state of the enzyme.


    Organizational Affiliation

    Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate carbamoyltransferase catalytic chain
A, C
310Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pyrB
EC: 2.1.3.2
Find proteins for P0A786 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A786
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aspartate carbamoyltransferase regulatory chain
B, D
153Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pyrI
Find proteins for P0A7F3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7F3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CTP
Query on CTP

Download SDF File 
Download CCD File 
B, D
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
EOB
Query on EOB

Download SDF File 
Download CCD File 
A, C
{1,3-PHENYLENEBIS[IMINO(2-OXOETHANE-2,1-DIYL)]}BIS(PHOSPHONIC ACID)
2,2'-(1,3-PHENYLENEBIS(AZANEDIYL))BIS(2-OXOETHANE-2,1DIYL)DIPHOSPHONIC ACID
C10 H14 N2 O8 P2
BHGKTXYPXMTFLT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EOBIC50: 86000 nM BINDINGMOAD
EOBKi: 420000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.940α = 90.00
b = 119.940β = 90.00
c = 141.970γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
AMoREphasing
CNSrefinement
d*TREKdata reduction
CrystalCleardata collection
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance