4YBG | pdb_00004ybg

Crystal structure of the MAEL domain of Drosophila melanogaster Maelstrom

• PDB DOI: https://doi.org/10.2210/pdb4YBG/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-02-18 Released: 2015-04-29 
• Deposition Author(s): Matsumoto, N., Ishitani, R., Nishimasu, H., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure and Activity of the Endoribonuclease Domain of the piRNA Pathway Factor Maelstrom

Matsumoto, N., Sato, K., Nishimasu, H., Namba, Y., Miyakubi, K., Dohmae, N., Ishitani, R., Siomi, H., Siomi, M.C., Nureki, O.

(2015) Cell Rep 11: 366-375

• PubMed: 25865890 
• DOI: https://doi.org/10.1016/j.celrep.2015.03.030
• Primary Citation Related Structures: 
  4YBG


• PubMed Abstract: 
  

  PIWI-interacting RNAs (piRNAs) protect the genome from transposons in animal gonads. Maelstrom (Mael) is an evolutionarily conserved protein, composed of a high-mobility group (HMG) domain and a MAEL domain, and is essential for piRNA-mediated transcriptional transposon silencing in various species, such as Drosophila and mice. However, its structure and biochemical function have remained elusive. Here, we report the crystal structure of the MAEL domain from Drosophila melanogaster Mael, at 1.6 Å resolution. The structure reveals that the MAEL domain has an RNase H-like fold but lacks canonical catalytic residues conserved among RNase H-like superfamily nucleases. Our biochemical analyses reveal that the MAEL domain exhibits single-stranded RNA (ssRNA)-specific endonuclease activity. Our cell-based analyses further indicate that ssRNA cleavage activity appears dispensable for piRNA-mediated transcriptional transposon silencing in Drosophila. Our findings provide clues toward understanding the multiple roles of Mael in the piRNA pathway.

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Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan; JST, PRESTO, Tokyo 113-0032, Japan.
Biomolecular Characterization Team and CREST/JST, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan. Electronic address: [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.29 kDa 
• Atom Count: 1,993 
• Modeled Residue Count: 238 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein maelstrom	A	255	Drosophila melanogaster	Mutation(s): 1  Gene Names: mael, CG11254
UniProt
Find proteins for Q9VNS0 (Drosophila melanogaster) Explore Q9VNS0  Go to UniProtKB:  Q9VNS0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.892	α = 90
b = 71.892	β = 90
c = 88.389	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SHARP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Matsumoto, N., Ishitani, R., Nishimasu, H., Nureki, O.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2015-05-06
  Changes: Database references
• Version 1.2: 2020-02-05
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description