6RVZ | pdb_00006rvz

Crystal structure of ANGEL2, a 2',3'-cyclic phosphatase, in complex with adenosine-2',3'-vanadate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.211 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KL2Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

ANGEL2 is a member of the CCR4 family of deadenylases with 2',3'-cyclic phosphatase activity.

Pinto, P.H.Kroupova, A.Schleiffer, A.Mechtler, K.Jinek, M.Weitzer, S.Martinez, J.

(2020) Science 369: 524-530

  • DOI: https://doi.org/10.1126/science.aba9763
  • Primary Citation of Related Structures:  
    6RVZ, 6RW0

  • PubMed Abstract: 

    RNA molecules are frequently modified with a terminal 2',3'-cyclic phosphate group as a result of endonuclease cleavage, exonuclease trimming, or de novo synthesis. During pre-transfer RNA (tRNA) and unconventional messenger RNA (mRNA) splicing, 2',3'-cyclic phosphates are substrates of the tRNA ligase complex, and their removal is critical for recycling of tRNAs upon ribosome stalling. We identified the predicted deadenylase angel homolog 2 (ANGEL2) as a human phosphatase that converts 2',3'-cyclic phosphates into 2',3'-OH nucleotides. We analyzed ANGEL2's substrate preference, structure, and reaction mechanism. Perturbing ANGEL2 expression affected the efficiency of pre-tRNA processing, X-box-binding protein 1 ( XBP1 ) mRNA splicing during the unfolded protein response, and tRNA nucleotidyltransferase 1 (TRNT1)-mediated CCA addition onto tRNAs. Our results indicate that ANGEL2 is involved in RNA pathways that rely on the ligation or hydrolysis of 2',3'-cyclic phosphates.


  • Organizational Affiliation

    Max Perutz Labs, Medical University of Vienna, Vienna BioCenter, 1030 Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein angel homolog 2429Homo sapiensMutation(s): 0 
Gene Names: ANGEL2KIAA0759L
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VTE6 (Homo sapiens)
Explore Q5VTE6 
Go to UniProtKB:  Q5VTE6
PHAROS:  Q5VTE6
GTEx:  ENSG00000174606 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VTE6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KL2 (Subject of Investigation/LOI)
Query on KL2

Download Ideal Coordinates CCD File 
B [auth A]adenosine-2',3'-vanadate
C10 H14 N5 O7 V
VVVFQERUKYCTSH-KWIZKVQNSA-K
ADN
Query on ADN

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.211 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.653α = 90
b = 99.653β = 90
c = 94.155γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KL2Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description