1R0C

Products in the T State of Aspartate Transcarbamylase: Crystal Structure of the Phosphate and N-carbamyl-L-aspartate Ligated Enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Products in the T-State of Aspartate Transcarbamylase: Crystal Structure of the Phosphate and N-Carbamyl-l-aspartate Ligated Enzyme

Huang, J.Lipscomb, W.N.

(2004) Biochemistry 43: 6422-6426

  • DOI: 10.1021/bi0302144

  • PubMed Abstract: 
  • The structure of aspartate transcarbamylase of Escherichia coli ligated to products (phosphate and N-carbamyl-l-aspartate) has been determined at 2.37 A resolution (R-factor = 0.23, R(free) = 0.27). Results might indicate a product release mode, rath ...

    The structure of aspartate transcarbamylase of Escherichia coli ligated to products (phosphate and N-carbamyl-l-aspartate) has been determined at 2.37 A resolution (R-factor = 0.23, R(free) = 0.27). Results might indicate a product release mode, rather than close analogues to the transition state like those found in our earlier studies of other ligands (N-phosphonacetyl-L-aspartate, carbamyl phosphate plus malonate, phosphonoacetamide plus malonate, or citrate plus phosphate). Ordered product release, first carbamylaspartate (CLA) and then phosphate, might be facilitated by a 4 A movement of phosphate from the substrate-analogue position to the product (phosphate) binding position, and by a somewhat similar release movement of the other product (CLA) relative to its analogue (citrate). This movement is consistent with earlier studies of binding of either pyrophosphate or phosphate alone [Honzatko, R. B., and Lipscomb, W. N. (1982) J. Mol. Biol. 160, 265-286].


    Related Citations: 
    • Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1A
      Jin, L.,Stec, B.,Lipscomb, W.N.,Kantrowitz, E.R.
      (1999) Proteins 37: 729
    • A single mutation in the regulatory chanin of Escherichia coli aspartate transcarbamoylase results in an extreme T-state structure
      Williams, M.K.,Stec, B.,Kantrowitz, E.R.
      (1998) J.Mol.Biol. 281: 121
    • Structural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6A resolution
      Stevens, R.C.,Gouaux, J.E.,Lipscomb, W.N.
      (1990) Biochemistry 29: 7691


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate carbamoyltransferase catalytic chain
A, G
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, H
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
NCD
Query on NCD

Download SDF File 
Download CCD File 
A, G
N-CARBAMOYL-L-ASPARTATE
C5 H8 N2 O5
HLKXYZVTANABHZ-REOHCLBHSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, G
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.226 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 128.776α = 90.00
b = 128.776β = 90.00
c = 198.017γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
HKL-2000data reduction
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance