PDBsum entry 2w6d

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Hydrolase PDB id
Protein chains
680 a.a. *
CPL ×44
GDP ×2
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Bacterial dynamin-like protein lipid tube bound
Structure: Dynamin family protein. Chain: a, b. Synonym: bacterial dynamin-like protein bdlp. Engineered: yes
Source: Nostoc punctiforme. Organism_taxid: 63737. Atcc: 29133. Expressed in: escherichia coli. Expression_system_taxid: 562
Authors: H.H.Low,C.Sachse,L.A.Amos,J.Lowe
Key ref:
H.H.Low et al. (2009). Structure of a bacterial dynamin-like protein lipid tube provides a mechanism for assembly and membrane curving. Cell, 139, 1342-1352. PubMed id: 20064379 DOI: 10.1016/j.cell.2009.11.003
18-Dec-08     Release date:   22-Dec-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
B2IZD3  (B2IZD3_NOSP7) -  Bacterial dynamin-like protein
693 a.a.
680 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.  - Dynamin GTPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP + H2O = GDP + phosphate
+ H(2)O
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     metabolic process   2 terms 
  Biochemical function     nucleotide binding     5 terms  


DOI no: 10.1016/j.cell.2009.11.003 Cell 139:1342-1352 (2009)
PubMed id: 20064379  
Structure of a bacterial dynamin-like protein lipid tube provides a mechanism for assembly and membrane curving.
H.H.Low, C.Sachse, L.A.Amos, J.Löwe.
Proteins of the dynamin superfamily mediate membrane fission, fusion, and restructuring events by polymerizing upon lipid bilayers and forcing regions of high curvature. In this work, we show the electron cryomicroscopy reconstruction of a bacterial dynamin-like protein (BDLP) helical filament decorating a lipid tube at approximately 11 A resolution. We fitted the BDLP crystal structure and produced a molecular model for the entire filament. The BDLP GTPase domain dimerizes and forms the tube surface, the GTPase effector domain (GED) mediates self-assembly, and the paddle region contacts the lipids and promotes curvature. Association of BDLP with GMPPNP and lipid induces radical, large-scale conformational changes affecting polymerization. Nucleotide hydrolysis seems therefore to be coupled to polymer disassembly and dissociation from lipid, rather than membrane restructuring. Observed structural similarities with rat dynamin 1 suggest that our results have broad implication for other dynamin family members.
  Selected figure(s)  
Figure 2.
Figure 2. Native and SAM-Labeled Helical Reconstruction of BDLP-GMPPNP Lipid Tubes by Single-Particle Methods at 11.0 Å and 16.9 Å Resolution, Respectively
(A) Density surface overview of the native BDLP tube reconstruction. Red dumbbells show zigzag arrangement of the dimeric asymmetric unit.
(B) As in (A), but sliced along the tube axis exposing the globular outer layer, inner radial spokes, and lipid tube core (red).
(C) As in (A), but showing the tube in cross-section to the helix axis. The lipid core is in red.
(D) Close-up view of region outlined in yellow in (C), showing surface detailing of the asymmetric unit and two-fold symmetry.
(E) As in (A), but a close-up view of the asymmetric unit showing surface detail.
(F) Density surface overview of the BDLP tube reconstruction incorporating the human p73α SAM-domain as a label, fused between neck and trunk.
(G) Close-up view of the region outlined in yellow in (F).
(H) Superposition of native (blue) and labeled (orange) reconstructions filtered to a resolution of 16 Å. Note the additional bridge of orange density between radial spokes attributed to the label.
(I) As in (H) but showing region enclosed by dotted lines. The unexpected thinness of the orange density bridge is thought to be due to label flexibility.
Figure 6.
Figure 6. Model of the BDLP-GMPPNP Helical Filament Shows Protein-Protein Contacts and Mechanism of Lipid Curvature
(A) Model of the helical BDLP filament in cross-section to the helix axis showing a fitted lipid bilayer. Only the inner ring of the lipid head groups (and hence lipids) is clearly observed in the 3D density, although the averaged density profile (Figure 3D) shows two sharp peaks that agree with direct end-on views (Figure 3C). The outer leaflet may not stand out in 3D because the ring of head groups is disrupted by the BDLP trunk tips and/or the bilayer is compressed to about half its natural thickness. A standard outer leaflet (5 nm bilayer thickness) is modeled for size comparison only. Shown close up are protein-protein contacts between a pair of asymmetric units. The focus is on interaction between the central neighboring neck and trunk helices.
(B) Surface view of the BDLP filament model. Shown close up is the arrangement of three dimeric asymmetric units within the helix. Polymerization arises through longitudinal back-to-back contacts between GTPase domains, between neck and trunk helices, plus lateral association of H4 helices. The disordered switch 2 region is represented by a dashed orange line. Note that the lateral contact is smaller, probably leading to unwinding in Figure 4K.
(C) Side and top view superposition of BDLP-GDP (Low and Löwe [2006], residues 68–348, colored cyan although helix 13 colored blue for clarity), BDLP-GMPPNP model (this study, lipid-bound form, residues 68–348, mainly colored green although helix 12 is colored orange), and rat dynamin 1 (nucleotide free, residues 33–304, colored red). Note how BDLP helix 12 and rat helix α5 are almost identically positioned and run in phase. The kink in helix α5 corroborates the BDLP-GMPPNP tube reconstruction, which suggests that helices 12 and 13 separate and act as a hinge (in the BDLP crystal structure H12 and H13 are almost continuous).
(D) Side view of the rat GTPase domain (residues 2–304) compared to the BDLP-GMPPNP GTPase domain with the kink between helices 12 and 13 modeled. The bending between helices 12 and 13 is observed in the equivalent rat helix α5. Also note how the N termini of the GTPase domains in both rat (2–33) and BDLP (2–68) contribute to the formation of a hydrophobic groove that seats the GED in BDLP. Rat Pro 32 is situated in the equivalent position to BDLP Gly 68 (Hinge 2a), suggesting the rat GTPase domain may also show flexibility around this region and the kink in helix α5.
  The above figures are reprinted by permission from Cell Press: Cell (2009, 139, 1342-1352) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22233676 S.M.Ferguson, and P.De Camilli (2012).
Dynamin, a membrane-remodelling GTPase.
  Nat Rev Mol Cell Biol, 13, 75-88.  
21205012 F.Bürmann, N.Ebert, S.van Baarle, and M.Bramkamp (2011).
A bacterial dynamin-like protein mediating nucleotide-independent membrane fusion.
  Mol Microbiol, 79, 1294-1304.  
21170049 J.A.Mears, L.L.Lackner, S.Fang, E.Ingerman, J.Nunnari, and J.E.Hinshaw (2011).
Conformational changes in Dnm1 support a contractile mechanism for mitochondrial fission.
  Nat Struct Mol Biol, 18, 20-26.  
21278333 O.Daumke, and G.J.Praefcke (2011).
Structural insights into membrane fusion at the endoplasmic reticulum.
  Proc Natl Acad Sci U S A, 108, 2175-2176.  
20837154 R.Ramachandran (2011).
Vesicle scission: dynamin.
  Semin Cell Dev Biol, 22, 10-17.  
21054581 S.I.Galkina, J.M.Romanova, E.E.Bragina, I.G.Tiganova, V.I.Stadnichuk, N.V.Alekseeva, V.Y.Polyakov, and T.Klein (2011).
Membrane tubules attach Salmonella Typhimurium to eukaryotic cells and bacteria.
  FEMS Immunol Med Microbiol, 61, 114-124.  
21368113 X.Bian, R.W.Klemm, T.Y.Liu, M.Zhang, S.Sun, X.Sui, X.Liu, T.A.Rapoport, and J.Hu (2011).
Structures of the atlastin GTPase provide insight into homotypic fusion of endoplasmic reticulum membranes.
  Proc Natl Acad Sci U S A, 108, 3976-3981.
PDB codes: 3qnu 3qof
21059949 D.Schwefel, C.Fröhlich, J.Eichhorst, B.Wiesner, J.Behlke, L.Aravind, and O.Daumke (2010).
Structural basis of oligomerization in septin-like GTPase of immunity-associated protein 2 (GIMAP2).
  Proc Natl Acad Sci U S A, 107, 20299-20304.
PDB codes: 2xtm 2xtn 2xto 2xtp
20585624 H.Ashrafian, L.Docherty, V.Leo, C.Towlson, M.Neilan, V.Steeples, C.A.Lygate, T.Hough, S.Townsend, D.Williams, S.Wells, D.Norris, S.Glyn-Jones, J.Land, I.Barbaric, Z.Lalanne, P.Denny, D.Szumska, S.Bhattacharya, J.L.Griffin, I.Hargreaves, N.Fernandez-Fuentes, M.Cheeseman, H.Watkins, and T.N.Dear (2010).
A mutation in the mitochondrial fission gene Dnm1l leads to cardiomyopathy.
  PLoS Genet, 6, e1001000.  
20700106 J.A.Kenniston, and M.A.Lemmon (2010).
Dynamin GTPase regulation is altered by PH domain mutations found in centronuclear myopathy patients.
  EMBO J, 29, 3054-3067.  
20428113 J.S.Chappie, S.Acharya, M.Leonard, S.L.Schmid, and F.Dyda (2010).
G domain dimerization controls dynamin's assembly-stimulated GTPase activity.
  Nature, 465, 435-440.
PDB codes: 2x2e 2x2f
20541505 V.M.Korkhov, C.Sachse, J.M.Short, and C.G.Tate (2010).
Three-dimensional structure of TspO by electron cryomicroscopy of helical crystals.
  Structure, 18, 677-687.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.