4H1U

Nucleotide-free human dynamin-1-like protein GTPase-GED fusion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functional Mapping of Human Dynamin-1-Like GTPase Domain Based on X-ray Structure Analyses.

Wenger, J.Klinglmayr, E.Frohlich, C.Eibl, C.Gimeno, A.Hessenberger, M.Puehringer, S.Daumke, O.Goettig, P.

(2013) Plos One 8: e71835-e71835

  • DOI: 10.1371/journal.pone.0071835
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human dynamin-1-like protein (DNM1L) is a GTP-driven molecular machine that segregates mitochondria and peroxisomes. To obtain insights into its catalytic mechanism, we determined crystal structures of a construct comprising the GTPase domain and the ...

    Human dynamin-1-like protein (DNM1L) is a GTP-driven molecular machine that segregates mitochondria and peroxisomes. To obtain insights into its catalytic mechanism, we determined crystal structures of a construct comprising the GTPase domain and the bundle signaling element (BSE) in the nucleotide-free and GTP-analogue-bound states. The GTPase domain of DNM1L is structurally related to that of dynamin and binds the nucleotide 5'-Guanylyl-imidodiphosphate (GMP-PNP) via five highly conserved motifs, whereas the BSE folds into a pocket at the opposite side. Based on these structures, the GTPase center was systematically mapped by alanine mutagenesis and kinetic measurements. Thus, residues essential for the GTPase reaction were characterized, among them Lys38, Ser39 and Ser40 in the phosphate binding loop, Thr59 from switch I, Asp146 and Gly149 from switch II, Lys216 and Asp218 in the G4 element, as well as Asn246 in the G5 element. Also, mutated Glu81 and Glu82 in the unique 16-residue insertion of DNM1L influence the activity significantly. Mutations of Gln34, Ser35, and Asp190 in the predicted assembly interface interfered with dimerization of the GTPase domain induced by a transition state analogue and led to a loss of the lipid-stimulated GTPase activity. Our data point to related catalytic mechanisms of DNM1L and dynamin involving dimerization of their GTPase domains.


    Organizational Affiliation

    Department of Molecular Biology, University of Salzburg, Salzburg, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dynamin-1-like protein
A
369Homo sapiensMutation(s): 0 
Gene Names: DNM1L (DLP1, DRP1)
EC: 3.6.5.5
Find proteins for O00429 (Homo sapiens)
Go to Gene View: DNM1L
Go to UniProtKB:  O00429
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.500α = 90.00
b = 151.430β = 90.00
c = 42.760γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Refinement description, Source and taxonomy