6NXA

ECAII(T89V,K162T) MUTANT IN COMPLEX WITH CITRATE AT PH 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Opportunistic complexes of E. coli L-asparaginases with citrate anions.

Lubkowski, J.Chan, W.Wlodawer, A.

(2019) Sci Rep 9: 11070-11070

  • DOI: 10.1038/s41598-019-46432-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Active sites of enzymes are highly optimized for interactions with specific substrates, thus binding of opportunistic ligands is usually observed only in the absence of native substrates or products. However, during growth of crystals required for st ...

    Active sites of enzymes are highly optimized for interactions with specific substrates, thus binding of opportunistic ligands is usually observed only in the absence of native substrates or products. However, during growth of crystals required for structure determination enzymes are often exposed to conditions significantly divergent from the native ones, leading to binding of unexpected ligands to active sites even in the presence of substrates. Failing to recognize this possibility may lead to incorrect interpretation of experimental results and to faulty conclusions. Here, we present several examples of binding of a citrate anion to the active sites of E. coli L-asparaginases I and II, even in the presence of the native substrate, L-Asn. A part of this report focuses on a comprehensive re-interpretation of structural results published previously for complexes of type I L-asparaginase (EcAI) from E. coli. In two re-refined structures a citrate anion forms an acyl-enzyme reaction intermediate with the catalytic threonine. These results emphasize the importance of careful and critical analysis during interpretation of crystallographic data.


    Related Citations: 
    • Crystal structure and allosteric regulation of the cytoplasmic Escherichia coli L-asparaginase I.
      Yun, M.K.,Nourse, A.,White, S.W.,Rock, C.O.,Heath, R.J.
      (2007) J. Mol. Biol. 369: 794


    Organizational Affiliation

    Department of Bioinformatics and Computational Biology and The Proteomics and Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA. lubkowsj@mail.nih.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-asparaginase 2
A, B, C, D
333Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: ansB
EC: 3.5.1.1
Find proteins for P00805 (Escherichia coli (strain K12))
Go to UniProtKB:  P00805
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, B, C, D
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 151.885α = 90.00
b = 62.509β = 118.19
c = 143.160γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-11-20
    Type: Database references