5LDM

Crystal structure of E.coli LigT complexed with 2'-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.

Myllykoski, M.Kursula, P.

(2017) PLoS One 12: e0170355-e0170355

  • DOI: 10.1371/journal.pone.0170355
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The 2H phosphoesterase family contains enzymes with two His-X-Ser/Thr motifs in the active site. 2H enzymes are found in all kingdoms of life, sharing little sequence identity despite the conserved overall fold and active site. For many 2H enzymes, t ...

    The 2H phosphoesterase family contains enzymes with two His-X-Ser/Thr motifs in the active site. 2H enzymes are found in all kingdoms of life, sharing little sequence identity despite the conserved overall fold and active site. For many 2H enzymes, the physiological function is unknown. Here, we studied the structure of the 2H family member LigT from Escherichia coli both in the apo form and complexed with different active-site ligands, including ATP, 2'-AMP, 3'-AMP, phosphate, and NADP+. Comparisons to the well-characterized vertebrate myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) highlight specific features of the catalytic cycle and substrate recognition in both enzymes. The role played by the helix α7, unique to CNPases within the 2H family, is apparently taken over by Arg130 in the bacterial enzyme. Other residues and loops lining the active site groove are likely to be important for RNA substrate binding. We visualized conformational changes related to ligand binding, as well as the position of the nucleophilic water molecule. We also present a low-resolution model of E. coli LigT bound to tRNA in solution, and provide a model for RNA binding by LigT, involving flexible loops lining the active site cavity. Taken together, our results both aid in understanding the common features of 2H family enzymes and help highlight the distinct features in the 2H family members, which must result in different reaction mechanisms. Unique aspects in different 2H family members can be observed in ligand recognition and binding, and in the coordination of the nucleophilic water molecule and the reactive phosphate moiety.


    Organizational Affiliation

    Department of Biomedicine, University of Bergen, Bergen, Norway.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA 2',3'-cyclic phosphodiesteraseA, B177Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: thpRECBD_3472
EC: 3.1.4 (PDB Primary Data), 3.1.4.58 (UniProt)
Find proteins for A0A140NFI1 (Escherichia coli (strain B / BL21-DE3))
Explore A0A140NFI1 
Go to UniProtKB:  A0A140NFI1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2AM
Query on 2AM

Download CCD File 
A, B
ADENOSINE-2'-MONOPHOSPHATE
C10 H14 N5 O7 P
QDFHPFSBQFLLSW-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2AMKd:  140000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.203 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.07α = 90
b = 108.07β = 90
c = 72.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection