6YWN

CutA in complex with CMPCPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine.

Malik, D.Kobylecki, K.Krawczyk, P.Poznanski, J.Jakielaszek, A.Napiorkowska, A.Dziembowski, A.Tomecki, R.Nowotny, M.

(2020) Nucleic Acids Res 48: 9387-9405

  • DOI: https://doi.org/10.1093/nar/gkaa647
  • Primary Citation of Related Structures:  
    6YWN, 6YWO, 6YWP

  • PubMed Abstract: 

    Template-independent terminal ribonucleotide transferases (TENTs) catalyze the addition of nucleotide monophosphates to the 3'-end of RNA molecules regulating their fate. TENTs include poly(U) polymerases (PUPs) with a subgroup of 3' CUCU-tagging enzymes, such as CutA in Aspergillus nidulans. CutA preferentially incorporates cytosines, processively polymerizes only adenosines and does not incorporate or extend guanosines. The basis of this peculiar specificity remains to be established. Here, we describe crystal structures of the catalytic core of CutA in complex with an incoming non-hydrolyzable CTP analog and an RNA with three adenosines, along with biochemical characterization of the enzyme. The binding of GTP or a primer with terminal guanosine is predicted to induce clashes between 2-NH2 of the guanine and protein, which would explain why CutA is unable to use these ligands as substrates. Processive adenosine polymerization likely results from the preferential binding of a primer ending with at least two adenosines. Intriguingly, we found that the affinities of CutA for the CTP and UTP are very similar and the structures did not reveal any apparent elements for specific NTP binding. Thus, the properties of CutA likely result from an interplay between several factors, which may include a conformational dynamic process of NTP recognition.


  • Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw 02-109, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CutA363Thermothielavioides terrestris NRRL 8126Mutation(s): 0 
Gene Names: THITE_2112714
UniProt
Find proteins for G2R014 (Thermothielavioides terrestris (strain ATCC 38088 / NRRL 8126))
Explore G2R014 
Go to UniProtKB:  G2R014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2R014
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2TM (Subject of Investigation/LOI)
Query on 2TM

Download Ideal Coordinates CCD File 
C [auth A]5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
C10 H18 N3 O13 P3
STGUOVSTMBLHFT-ZOQUXTDFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.22α = 90
b = 93.47β = 90
c = 86.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Foundation for Polish SciencePolandPOIR.04.04.00-00-20E7/16-00

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-09-30
    Changes: Database references