6DU4 | pdb_00006du4

Crystal structure of hMettl16 catalytic domain in complex with MAT2A 3'UTR hairpin 1

• PDB DOI: https://doi.org/10.2210/pdb6DU4/pdb
• NAKB: 6DU4

• Classification: Transferase/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-19 Released: 2018-09-26 
• Deposition Author(s): Doxtader, K., Wang, P., Nam, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: other

Literature

Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor.

Doxtader, K.A., Wang, P., Scarborough, A.M., Seo, D., Conrad, N.K., Nam, Y.

(2018) Mol Cell 71: 1001-1011.e4

• PubMed: 30197297 
• DOI: https://doi.org/10.1016/j.molcel.2018.07.025
• Primary Citation Related Structures: 
  6DU4, 6DU5


• PubMed Abstract: 
  

  S-adenosylmethionine (SAM) is an essential metabolite that acts as a cofactor for most methylation events in the cell. The N ⁶ -methyladenosine (m ⁶ A) methyltransferase METTL16 controls SAM homeostasis by regulating the abundance of SAM synthetase MAT2A mRNA in response to changing intracellular SAM levels. Here we present crystal structures of METTL16 in complex with MAT2A RNA hairpins to uncover critical molecular mechanisms underlying the regulated activity of METTL16. The METTL16-RNA complex structures reveal atomic details of RNA substrates that drive productive methylation by METTL16. In addition, we identify a polypeptide loop in METTL16 near the SAM binding site with an autoregulatory role. We show that mutations that enhance or repress METTL16 activity in vitro correlate with changes in MAT2A mRNA levels in cells. Thus, we demonstrate the structural basis for the specific activity of METTL16 and further suggest the molecular mechanisms by which METTL16 efficiency is tuned to regulate SAM homeostasis.

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Organizational Affiliation: 
• Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. 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)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 45.58 kDa 
• Atom Count: 3,422 
• Modeled Residue Count: 316 
• Deposited Residue Count: 342 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase	A	313	Homo sapiens	Mutation(s): 0  Gene Names: METTL16, METT10D EC: 2.1.1.346 (PDB Primary Data), 2.1.1.62 (PDB Primary Data), 2.1.1.348 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86W50 (Homo sapiens) Explore Q86W50  Go to UniProtKB:  Q86W50
PHAROS:  Q86W50 GTEx:  ENSG00000127804

Entity ID: 2
Molecule	Chains	Length	Organism	Image
hp1x-RNA (29-MER)	B	29	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A], F [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.979	α = 90
b = 74.979	β = 90
c = 93.213	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Doxtader, K., Wang, P., Nam, Y.

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Funding Organization	Location	Grant Number
	United States	--

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2018-10-03
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description