5COT

Structure and mechanism of a eukaryal nick-sealing RNA ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase.

Unciuleac, M.C.Goldgur, Y.Shuman, S.

(2015) Proc.Natl.Acad.Sci.USA 112: 13868-13873

  • DOI: 10.1073/pnas.1516536112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ATP-dependent RNA ligases are agents of RNA repair that join 3'-OH and 5'-PO4 RNA ends. Naegleria gruberi RNA ligase (NgrRnl) exemplifies a family of RNA nick-sealing enzymes found in bacteria, viruses, and eukarya. Crystal structures of NgrRnl at th ...

    ATP-dependent RNA ligases are agents of RNA repair that join 3'-OH and 5'-PO4 RNA ends. Naegleria gruberi RNA ligase (NgrRnl) exemplifies a family of RNA nick-sealing enzymes found in bacteria, viruses, and eukarya. Crystal structures of NgrRnl at three discrete steps along the reaction pathway-covalent ligase-(lysyl-Nζ)-AMP•Mn(2+) intermediate; ligase•ATP•(Mn(2+))2 Michaelis complex; and ligase•Mn(2+) complex-highlight a two-metal mechanism of nucleotidyl transfer, whereby (i) an enzyme-bound "catalytic" metal coordination complex lowers the pKa of the lysine nucleophile and stabilizes the transition state of the ATP α phosphate; and (ii) a second metal coordination complex bridges the β- and γ-phosphates. The NgrRnl N domain is a distinctively embellished oligonucleotide-binding (OB) fold that engages the γ-phosphate and associated metal complex and orients the pyrophosphate leaving group for in-line catalysis with stereochemical inversion at the AMP phosphate. The unique domain architecture of NgrRnl fortifies the theme that RNA ligases have evolved many times, and independently, by fusions of a shared nucleotidyltransferase domain to structurally diverse flanking modules. The mechanistic insights to lysine adenylylation gained from the NgrRnl structures are likely to apply broadly to the covalent nucleotidyltransferase superfamily of RNA ligases, DNA ligases, and RNA capping enzymes.


    Organizational Affiliation

    Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065; s-shuman@ski.mskcc.org.,Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065;,Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Naegleria gruberi RNA ligase
A
340Naegleria gruberiMutation(s): 0 
Find proteins for D2W2Z5 (Naegleria gruberi)
Go to UniProtKB:  D2W2Z5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.158 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 55.285α = 90.00
b = 55.285β = 90.00
c = 102.545γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM42498

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references
  • Version 1.2: 2015-11-25
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations