|Entry||Database: PDB / ID: 5ljw|
|Title||MamK non-polymerising A278D mutant bound to AMPPNP|
|Keywords||HYDROLASE / bacterial cytoskeleton / filamentous protein / actin-like / magnetosomes|
|Function / homology|
Function and homology information
biomineralization / magnetosome membrane / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / hydrolase activity / cytoskeleton / ATP hydrolysis activity / GTP binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
MreB/Mbl protein / Actin / Actin family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Actin-like protein MamK
Similarity search - Component
|Biological species||Magnetospirillum magneticum AMB-1 (magnetotactic)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å|
|Funding support|| United Kingdom, 2items |
|Citation||Journal: Proc Natl Acad Sci U S A / Year: 2016|
Title: X-ray and cryo-EM structures of monomeric and filamentous actin-like protein MamK reveal changes associated with polymerization.
Authors: Jan Löwe / Shaoda He / Sjors H W Scheres / Christos G Savva /
Abstract: Magnetotactic bacteria produce iron-rich magnetic nanoparticles that are enclosed by membrane invaginations to form magnetosomes so they are able to sense and act upon Earth's magnetic field. In ...Magnetotactic bacteria produce iron-rich magnetic nanoparticles that are enclosed by membrane invaginations to form magnetosomes so they are able to sense and act upon Earth's magnetic field. In Magnetospirillum and other magnetotactic bacteria, to combine their magnetic moments, magnetosomes align along filaments formed by a bacterial actin homolog, MamK. Here, we present the crystal structure of a nonpolymerizing mutant of MamK from Magnetospirillum magneticum AMB-1 at 1.8-Å resolution, revealing its close similarity to actin and MreB. The crystals contain AMPPNP-bound monomeric MamK in two different conformations. To investigate conformational changes associated with polymerization, we used unmodified MamK protein and cryo-EM with helical 3D reconstruction in RELION to obtain a density map and a fully refined atomic model of MamK in filamentous form at 3.6-Å resolution. The filament is parallel (polar) double-helical, with a rise of 52.2 Å and a twist of 23.8°. As shown previously and unusually for actin-like filaments, the MamK subunits from each of the two strands are juxtaposed, creating an additional twofold axis along the filament. Compared with monomeric MamK, ADP-bound MamK in the filament undergoes a conformational change, rotating domains I and II against each other to further close the interdomain cleft between subdomains IB and IIB. The domain movement causes several loops to close around the nucleotide-binding pocket. Glu-143, a key residue for catalysis coordinating the magnesium ion, moves closer, presumably switching nucleotide hydrolysis upon polymerization-one of the hallmarks of cytomotive filaments of the actin type.
|Structure viewer||Molecule: |
Downloads & links
A: Actin-like ATPase
B: Actin-like ATPase
A: Actin-like ATPase
B: Actin-like ATPase
Mass: 37686.160 Da / Num. of mol.: 2 / Mutation: A278D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magneticum AMB-1 (magnetotactic)
Gene: amb0965 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2W8Q6
|#2: Chemical||#3: Chemical|
Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
|#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 %|
|Crystal grow||Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 50 mM HEPES pH 7.3, 48 % (w/v) PEG 1000|
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97941 Å|
|Detector||Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2015|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.97941 Å / Relative weight: 1|
|Reflection||Resolution: 1.8→50 Å / Num. obs: 138054 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.9|
|Reflection shell||Resolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.81 / % possible all: 97.4|
|Refinement||Method to determine structure: SIRAS / Resolution: 1.8→44.858 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.71 / Phase error: 21.1 |
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å|
|Refinement step||Cycle: LAST / Resolution: 1.8→44.858 Å|
|Refine LS restraints|
|LS refinement shell|
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