5ZZW

Proteobacterial origin of protein arginine methylation and regulation of Complex I assembly by MidA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

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This is version 1.2 of the entry. See complete history


Literature

Proteobacterial Origin of Protein Arginine Methylation and Regulation of Complex I Assembly by MidA.

Shahul Hameed, U.F.S.Sanislav, O.Lay, S.T.Annesley, S.J.Jobichen, C.Fisher, P.R.Swaminathan, K.Arold, S.T.

(2018) Cell Rep 24: 1996-2004

  • DOI: 10.1016/j.celrep.2018.07.075
  • Primary Citation of Related Structures:  
    5ZTZ, 5ZU0, 5ZZW

  • PubMed Abstract: 
  • The human protein arginine methyltransferase NDUFAF7 controls the assembly of the ∼1-MDa mitochondrial complex I (CI; the NADH ubiquinone oxidoreductase) by methylating its subunit NDUFS2. We determined crystal structures of MidA, the Dictyostelium ortholog of NDUFAF7 ...

    The human protein arginine methyltransferase NDUFAF7 controls the assembly of the ∼1-MDa mitochondrial complex I (CI; the NADH ubiquinone oxidoreductase) by methylating its subunit NDUFS2. We determined crystal structures of MidA, the Dictyostelium ortholog of NDUFAF7. The MidA catalytic core domain resembles other eukaryotic methyltransferases. However, three large core loops assemble into a regulatory domain that is likely to control ligand selection. Binding of MidA to NDUFS2 is weakened by methylation, suggesting a mechanism for methylation-controlled substrate release. Structural and bioinformatic analyses support that MidA and NDUFAF7 and their role in CI assembly are conserved from bacteria to humans, implying that protein methylation already existed in proteobacteria. In vivo studies confirmed the critical role of the MidA methyltransferase activity for CI assembly, growth, and phototaxis of Dictyostelium. Collectively, our data elucidate the origin of protein arginine methylation and its use by MidA/NDUFAF7 to regulate CI assembly.


    Organizational Affiliation

    King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia. Electronic address: stefan.arold@kaust.edu.sa.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine methyltransferase NDUFAF7 homolog, mitochondrialB [auth A], A [auth B], C414Dictyostelium discoideumMutation(s): 0 
Gene Names: midADDB_G0282615
EC: 2.1.1.320
UniProt
Find proteins for Q54S83 (Dictyostelium discoideum)
Explore Q54S83 
Go to UniProtKB:  Q54S83
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
D [auth B], E [auth A], F [auth C]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.95α = 90
b = 103.54β = 90
c = 192.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-25
    Changes: Database references