4E80 | pdb_00004e80

Structural Basis for the Activity of a Cytoplasmic RNA Terminal U-transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 
    0.201 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural basis for the activity of a cytoplasmic RNA terminal uridylyl transferase.

Yates, L.A.Fleurdepine, S.Rissland, O.S.De Colibus, L.Harlos, K.Norbury, C.J.Gilbert, R.J.

(2012) Nat Struct Mol Biol 19: 782-787

  • DOI: https://doi.org/10.1038/nsmb.2329
  • Primary Citation Related Structures: 
    4E7X, 4E80, 4E8F

  • PubMed Abstract: 

    Cytoplasmic terminal uridylyl transferases comprise a conserved family of enzymes that negatively regulate the stability or biological activity of a variety of eukaryotic RNAs, including mRNAs and tumor-suppressor let-7 microRNAs. Here we describe crystal structures of the Schizosaccharomyces pombe cytoplasmic terminal uridylyl transferase Cid1 in two apo conformers and bound to UTP. We demonstrate that a single histidine residue, conserved in mammalian Cid1 orthologs, is responsible for discrimination between UTP and ATP. We also describe a new high-affinity RNA substrate-binding mechanism of Cid1, which is essential for enzymatic activity and is mediated by three basic patches across the surface of the enzyme. Overall, our structures provide a basis for understanding the activity of Cid1 and a mechanism of UTP selectivity conserved in its human orthologs, suggesting potential implications for anticancer drug design.


  • Organizational Affiliation
    • Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecule Content 

  • Total Structure Weight: 187.22 kDa 
  • Atom Count: 10,472 
  • Modeled Residue Count: 1,282 
  • Deposited Residue Count: 1,620 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly(A) RNA polymerase protein cid1
A, B, C, D
405Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cid1SPAC19D5.03
EC: 2.7.7 (PDB Primary Data), 2.7.7.19 (UniProt), 2.7.7.52 (UniProt)
UniProt
Find proteins for O13833 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13833 
Go to UniProtKB:  O13833
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13833
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free:  0.201 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.69α = 90
b = 77.96β = 109.29
c = 151.68γ = 90
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-07-18
    Changes: Database references
  • Version 1.2: 2012-08-22
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations