6NX7

ECAII(D90T,K162T) MUTANT IN COMPLEX WITH CITRATE AT PH 5.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.135 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    6NX9, 6NX8, 6NX7, 6NX6, 6NXA, 6NXC, 6NXB, 6NXD

  • 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 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 ...

    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

    Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-asparaginase 2A, B333Escherichia coli K-12Mutation(s): 1 
Gene Names: ansBb2957JW2924
EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12))
Explore P00805 
Go to UniProtKB:  P00805
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
D [auth B]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
C [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.135 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.199α = 90
b = 126.199β = 90
c = 89.439γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2020-08-19
    Changes: Structure summary