4WKG

The crystal structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic coop-erativity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic cooperativity.

Fischer, U.Hertlein, S.Grimm, C.

(2015) Acta Crystallogr.,Sect.D 71: 687-696

  • DOI: 10.1107/S1399004714026686

  • PubMed Abstract: 
  • The bacterial protein ArnA is an essential enzyme in the pathway leading to the modification of lipid A with the pentose sugar 4-amino-4-deoxy-L-arabinose. This modification confers resistance to polymyxins, which are antibiotics that are used as a l ...

    The bacterial protein ArnA is an essential enzyme in the pathway leading to the modification of lipid A with the pentose sugar 4-amino-4-deoxy-L-arabinose. This modification confers resistance to polymyxins, which are antibiotics that are used as a last resort to treat infections with multiple drug-resistant Gram-negative bacteria. ArnA contains two domains with distinct catalytic functions: a dehydrogenase domain and a transformylase domain. The protein forms homohexamers organized as a dimer of trimers. Here, the crystal structure of apo ArnA is presented and compared with its ATP- and UDP-glucuronic acid-bound counterparts. The comparison reveals major structural rearrangements in the dehydrogenase domain that lead to the formation of a previously unobserved binding pocket at the centre of each ArnA trimer in its apo state. In the crystal structure, this pocket is occupied by a DTT molecule. It is shown that formation of the pocket is linked to a cascade of structural rearrangements that emerge from the NAD(+)-binding site. Based on these findings, a small effector molecule is postulated that binds to the central pocket and modulates the catalytic properties of ArnA. Furthermore, the discovered conformational changes provide a mechanistic explanation for the strong cooperative effect recently reported for the ArnA dehydrogenase function.


    Organizational Affiliation

    Department of Biochemistry, Biocenter of the University of Würzburg, Am Hubland, 97074 Würzburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional polymyxin resistance protein ArnA
A, B, C, D, E, F
660Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: arnA (pmrI, yfbG)
Find proteins for P77398 (Escherichia coli (strain K12))
Go to UniProtKB:  P77398
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, F
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
DTT
Query on DTT

Download SDF File 
Download CCD File 
A, D
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 106.720α = 81.92
b = 112.820β = 82.96
c = 113.610γ = 83.80
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-10-02 
  • Released Date: 2014-12-17 
  • Deposition Author(s): Grimm, C.

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-03-11
    Type: Database references
  • Version 1.2: 2016-07-20
    Type: Database references