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 6LBJ | pdb_00006lbj

Structure of mouse GLD-2 (Terminal nucleotidyltransferase 2, TENT2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.271 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6LBJ

This is version 1.2 of the entry. See complete history. 

Literature

Structures of mammalian GLD-2 proteins reveal molecular basis of their functional diversity in mRNA and microRNA processing.

Ma, X.Y., Zhang, H., Feng, J.X., Hu, J.L., Yu, B., Luo, L., Cao, Y.L., Liao, S., Wang, J., Gao, S.

(2020) Nucleic Acids Res 48: 8782-8795

  • DOI: https://doi.org/10.1093/nar/gkaa578
  • Primary Citation Related Structures: 
    6LBJ, 6LBK

  • PubMed Abstract: 

    The stability and processing of cellular RNA transcripts are efficiently controlled via non-templated addition of single or multiple nucleotides, which is catalyzed by various nucleotidyltransferases including poly(A) polymerases (PAPs). Germline development defective 2 (GLD-2) is among the first reported cytoplasmic non-canonical PAPs that promotes the translation of germline-specific mRNAs by extending their short poly(A) tails in metazoan, such as Caenorhabditis elegans and Xenopus. On the other hand, the function of mammalian GLD-2 seems more diverse, which includes monoadenylation of certain microRNAs. To understand the structural basis that underlies the difference between mammalian and non-mammalian GLD-2 proteins, we determine crystal structures of two rodent GLD-2s. Different from C. elegans GLD-2, mammalian GLD-2 is an intrinsically robust PAP with an extensively positively charged surface. Rodent and C. elegans GLD-2s have a topological difference in the β-sheet region of the central domain. Whereas C. elegans GLD-2 prefers adenosine-rich RNA substrates, mammalian GLD-2 can work on RNA oligos with various sequences. Coincident with its activity on microRNAs, mammalian GLD-2 structurally resembles the mRNA and miRNA processor terminal uridylyltransferase 7 (TUT7). Our study reveals how GLD-2 structurally evolves to a more versatile nucleotidyltransferase, and provides important clues in understanding its biological function in mammals.


  • Organizational Affiliation: 
    • State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China.

Macromolecule Content 

  • Total Structure Weight: 84.75 kDa 
  • Atom Count: 5,322 
  • Modeled Residue Count: 652 
  • Deposited Residue Count: 736 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly(A) RNA polymerase GLD2
A, B
368Mus musculusMutation(s): 2 
Gene Names: Tent2, Gld2, Papd4
EC: 2.7.7.19
UniProt & NIH Common Fund Data Resources
Find proteins for Q91YI6 (Mus musculus)
Explore Q91YI6 
Go to UniProtKB:  Q91YI6
IMPC:  MGI:2140950
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91YI6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.271 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.277α = 87.381
b = 47.144β = 88.056
c = 105.446γ = 63.806
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description