6S0M

Structural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


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Literature

Structural and dynamic studies provide insights into specificity and allosteric regulation of ribonuclease as, a key enzyme in mycobacterial virulence.

Calvanese, L.Squeglia, F.Romano, M.D'Auria, G.Falcigno, L.Berisio, R.

(2019) J.Biomol.Struct.Dyn. --: 1-13

  • DOI: 10.1080/07391102.2019.1643786

  • PubMed Abstract: 
  • Ribonuclease AS (RNase AS) is a crucial enzyme for virulence of <i>Mycobacterium tuberculosis </i>. We previously observed that RNase AS structurally resembles RNase T from <i>Escherichia coli </i>, an important enzyme for tRNA maturation and turno ...

    Ribonuclease AS (RNase AS) is a crucial enzyme for virulence of Mycobacterium tuberculosis . We previously observed that RNase AS structurally resembles RNase T from Escherichia coli , an important enzyme for tRNA maturation and turnover. Here, we combine X-ray crystallography and molecular dynamics (MD) to investigate the specificity and dynamic properties of substrate binding. Both X-ray and MD data provide structural determinants that corroborate the strict substrate specificity of RNase AS to cleave only adenosine residues, due to the structural features of adenine base. Beside suggesting tRNA as most likely substrate of RNase AS, MD and modeling studies identify key enzyme-ligand interactions, both involving the catalytic site and the double helix region of tRNA, which is locked by interactions with a set of arginine residues. The MD data also evidence a ligand-induced conformational change of the enzyme which is transferred from one chain to the adjacent one. These data will explain the dimeric nature of both RNase AS and RNase T, with two catalytic grooves composed of both chains. Also, they account for the dichotomy of tRNA, which contains both the substrate poly(A) chain and an inhibiting double strand RNA. Indeed, they provide a possible mechanism of allosteric regulation, which unlocks one catalytic groove when the second groove is inhibited by the double strand region of tRNA. Finally, a full comprehension of the molecular details of tRNA maturation processes is essential to develop novel strategies to modulate RNA processing, for therapeutic purposes. Abbreviations MD molecular dynamics PDB Protein Data Bank RMSD root mean square deviation RMSF root mean square fluctuation RNA ribonucleotidic acid RNase AS Ribonuclease AS Communicated by Ramasamy H. Sarma.


    Organizational Affiliation

    b Department of Pharmacy, University of Naples Federico II , Naples , Italy.,c Institute of Bio-Structures and Bio-Imaging - CNR-IBB , Naples , Italy.,a CIRPeB, University of Naples Federico II , Naples , Italy.,d Department of Life Sciences, Imperial College London , London , UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3'-5' exoribonuclease
A, B
168Mycobacterium tuberculosisMutation(s): 0 
EC: 3.1.13.-
Find proteins for A0A045JQ63 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JQ63
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*G)-3')C2Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.464α = 90.00
b = 77.068β = 90.00
c = 104.572γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release