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PDBsum entry 1jx2

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1jx2
Jmol
Contents
Protein chains
753 a.a. *
281 a.a. *
Ligands
THR-ARG-GLY-LEU-
VAL
BGC
ADP
Metals
_MG
Waters ×376
* Residue conservation analysis
PDB id:
1jx2
Name: Hydrolase
Title: Crystal structure of the nucleotide-free dynamin a gtpase domain, determined as myosin fusion
Structure: Myosin ii heavy chain. Chain: a. Fragment: residues 3-765, catalytic domain. Engineered: yes. Dynamin a gtpase domain. Chain: b. Fragment: residues 2-316. Engineered: yes. Linker peptide.
Source: Dictyostelium discoideum. Organism_taxid: 44689. Expressed in: dictyostelium discoideum. Expression_system_taxid: 44689. Gene: dyma.
Biol. unit: Trimer (from PQS)
Resolution:
2.30Å     R-factor:   0.197     R-free:   0.255
Authors: H.H.Niemann,M.L.W.Knetsch,A.Scherer,D.J.Manstein,F.J.Kull
Key ref:
H.H.Niemann et al. (2001). Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms. EMBO J, 20, 5813-5821. PubMed id: 11689422 DOI: 10.1093/emboj/20.21.5813
Date:
05-Sep-01     Release date:   07-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08799  (MYS2_DICDI) -  Myosin-2 heavy chain
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2116 a.a.
753 a.a.*
Protein chain
Pfam   ArchSchema ?
Q94464  (DYNA_DICDI) -  Dynamin-A
Seq:
Struc:
 
Seq:
Struc:
853 a.a.
281 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     myosin complex   1 term 
  Biochemical function     ATP binding     4 terms  

 

 
DOI no: 10.1093/emboj/20.21.5813 EMBO J 20:5813-5821 (2001)
PubMed id: 11689422  
 
 
Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms.
H.H.Niemann, M.L.Knetsch, A.Scherer, D.J.Manstein, F.J.Kull.
 
  ABSTRACT  
 
Dynamins form a family of multidomain GTPases involved in endocytosis, vesicle trafficking and maintenance of mitochondrial morphology. In contrast to the classical switch GTPases, a force-generating function has been suggested for dynamins. Here we report the 2.3 A crystal structure of the nucleotide-free and GDP-bound GTPase domain of Dictyostelium discoideum dynamin A. The GTPase domain is the most highly conserved region among dynamins. The globular structure contains the G-protein core fold, which is extended from a six-stranded beta-sheet to an eight-stranded one by a 55 amino acid insertion. This topologically unique insertion distinguishes dynamins from other subfamilies of GTP-binding proteins. An additional N-terminal helix interacts with the C-terminal helix of the GTPase domain, forming a hydrophobic groove, which could be occupied by C-terminal parts of dynamin not present in our construct. The lack of major conformational changes between the nucleotide-free and the GDP-bound state suggests that mechanochemical rearrangements in dynamin occur during GTP binding, GTP hydrolysis or phosphate release and are not linked to loss of GDP.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Comparison of the nucleotide-binding site of empty and GDP-bound dynamin A with those of empty EF-G and GDP-bound Ras. (A) In nucleotide-free dynamin A, the side chain of Thr207 from the TKLD motif makes a hydrogen bond (dashed lines) to the carbonyl of Ser36 in the P-loop. Lys38 binds to residues from switch II (Asp138 and Leu139). (B) In GDP-bound dynamin A, Lys38 preserves its interactions with residues from switch II and does not bind to the -phosphate. Lys208 binds the endocyclic oxygen of the ribose and Asp210 makes two hydrogen bonds with the base, while Thr207 does not bind the base. The coordination of the Mg2+ (magenta), which is usually octahedral in G-proteins [see (D)], is non-standard due to the disorder of the structural elements and water molecules (cyan) in this region. (C) In nucleotide-free EF-G, the P-loop Lys25 binds to residues from switch II, as in dynamin A. Asn137, equivalent to dynamin A Thr207, interacts with the side chain of Thr28 in the helix following the P-loop. (D) The canonical nucleotide-binding site of Ras-GDP. Lys16 binds to the -phosphate. The interactions of Lys117 and Asp119 with the nucleotide correspond to those of Lys208 and Asp210 in dynamin A. Asn116 in Ras makes two hydrogen bonds, one to the carbonyl of Val14 in the P-loop and one to the base.
Figure 5.
Figure 5 Comparison of dynamin A Phe50 and Ras Phe28. Dynamin A is colored in orange and Ras in green. GDP is only shown for Ras. Gly47 at the end of helix 1 allows the switch I loop to take off at a different angle in dynamin A than in Ras, which has no glycine at the equivalent position. In dynamin A, Phe50 is buried by hydrophobic residues of the -sheet (not shown) instead of stabilizing the base as Ras Phe28 does. The position of the Ras G5 motif (145SAK147) and of dynamin A Asn238 and Arg 239 is also shown.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 5813-5821) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20837154 R.Ramachandran (2011).
Vesicle scission: dynamin.
  Semin Cell Dev Biol, 22, 10-17.  
20016007 B.He, X.Yu, M.Margolis, X.Liu, X.Leng, Y.Etzion, F.Zheng, N.Lu, F.A.Quiocho, D.Danino, and Z.Zhou (2010).
Live-cell imaging in Caenorhabditis elegans reveals the distinct roles of dynamin self-assembly and guanosine triphosphate hydrolysis in the removal of apoptotic cells.
  Mol Biol Cell, 21, 610-629.  
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
19638400 C.Figueroa-Romero, J.A.Iñiguez-Lluhí, J.Stadler, C.R.Chang, D.Arnoult, P.J.Keller, Y.Hong, C.Blackstone, and E.L.Feldman (2009).
SUMOylation of the mitochondrial fission protein Drp1 occurs at multiple nonconsensus sites within the B domain and is linked to its activity cycle.
  FASEB J, 23, 3917-3927.  
20064379 H.H.Low, C.Sachse, L.A.Amos, and J.Löwe (2009).
Structure of a bacterial dynamin-like protein lipid tube provides a mechanism for assembly and membrane curving.
  Cell, 139, 1342-1352.
PDB code: 2w6d
19515832 J.S.Chappie, S.Acharya, Y.W.Liu, M.Leonard, T.J.Pucadyil, and S.L.Schmid (2009).
An intramolecular signaling element that modulates dynamin function in vitro and in vivo.
  Mol Biol Cell, 20, 3561-3571.  
19437476 L.R.Odell, N.Chau, A.Mariana, M.E.Graham, P.J.Robinson, and A.McCluskey (2009).
Azido and diazarinyl analogues of bis-tyrphostin as asymmetrical inhibitors of dynamin GTPase.
  ChemMedChem, 4, 1182-1188.  
19424291 R.Gasper, S.Meyer, K.Gotthardt, M.Sirajuddin, and A.Wittinghofer (2009).
It takes two to tango: regulation of G proteins by dimerization.
  Nat Rev Mol Cell Biol, 10, 423-429.  
19469550 S.O.Shan, S.L.Schmid, and X.Zhang (2009).
Signal recognition particle (SRP) and SRP receptor: a new paradigm for multistate regulatory GTPases.
  Biochemistry, 48, 6696-6704.  
19445933 T.Uo, J.Dworzak, C.Kinoshita, D.M.Inman, Y.Kinoshita, P.J.Horner, and R.S.Morrison (2009).
Drp1 levels constitutively regulate mitochondrial dynamics and cell survival in cortical neurons.
  Exp Neurol, 218, 274-285.  
18780816 L.Corsini, M.Hothorn, K.Scheffzek, M.Sattler, and G.Stier (2008).
Thioredoxin as a fusion tag for carrier-driven crystallization.
  Protein Sci, 17, 2070-2079.  
18079695 R.Ramachandran, and S.L.Schmid (2008).
Real-time detection reveals that effectors couple dynamin's GTP-dependent conformational changes to the membrane.
  EMBO J, 27, 27-37.  
17853461 E.Kalay, A.Uzumcu, E.Krieger, R.Caylan, O.Uyguner, M.Ulubil-Emiroglu, H.Erdol, H.Kayserili, G.Hafiz, N.Başerer, A.J.Heister, H.C.Hennies, P.Nürnberg, S.Başaran, H.G.Brunner, C.W.Cremers, A.Karaguzel, B.Wollnik, and H.Kremer (2007).
MYO15A (DFNB3) mutations in Turkish hearing loss families and functional modeling of a novel motor domain mutation.
  Am J Med Genet A, 143, 2382-2389.  
17937909 J.A.Mears, P.Ray, and J.E.Hinshaw (2007).
A corkscrew model for dynamin constriction.
  Structure, 15, 1190-1202.  
17362197 S.Hoppins, L.Lackner, and J.Nunnari (2007).
The machines that divide and fuse mitochondria.
  Annu Rev Biochem, 76, 751-780.  
16511497 A.Ghosh, G.J.Praefcke, L.Renault, A.Wittinghofer, and C.Herrmann (2006).
How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP.
  Nature, 440, 101-104.
PDB codes: 2b8w 2b92 2bc9 2d4h
17122778 H.H.Low, and J.Löwe (2006).
A bacterial dynamin-like protein.
  Nature, 444, 766-769.
PDB codes: 2j68 2j69
15824135 R.Narayanan, M.Leonard, B.D.Song, S.L.Schmid, and M.Ramaswami (2005).
An internal GAP domain negatively regulates presynaptic dynamin in vivo: a two-step model for dynamin function.
  J Cell Biol, 169, 117-126.  
16218949 S.Thoms, and R.Erdmann (2005).
Dynamin-related proteins and Pex11 proteins in peroxisome division and proliferation.
  FEBS J, 272, 5169-5181.  
16141317 T.F.Reubold, S.Eschenburg, A.Becker, M.Leonard, S.L.Schmid, R.B.Vallee, F.J.Kull, and D.J.Manstein (2005).
Crystal structure of the GTPase domain of rat dynamin 1.
  Proc Natl Acad Sci U S A, 102, 13093-13098.
PDB code: 2aka
15004222 B.D.Song, D.Yarar, and S.L.Schmid (2004).
An assembly-incompetent mutant establishes a requirement for dynamin self-assembly in clathrin-mediated endocytosis in vivo.
  Mol Biol Cell, 15, 2243-2252.  
15262989 B.D.Song, M.Leonard, and S.L.Schmid (2004).
Dynamin GTPase domain mutants that differentially affect GTP binding, GTP hydrolysis, and clathrin-mediated endocytosis.
  J Biol Chem, 279, 40431-40436.  
15040446 G.J.Praefcke, and H.T.McMahon (2004).
The dynamin superfamily: universal membrane tubulation and fission molecules?
  Nat Rev Mol Cell Biol, 5, 133-147.  
15139810 J.Löwe, F.van den Ent, and L.A.Amos (2004).
Molecules of the bacterial cytoskeleton.
  Annu Rev Biophys Biomol Struct, 33, 177-198.  
15037301 L.A.Amos, F.van den Ent, and J.Löwe (2004).
Structural/functional homology between the bacterial and eukaryotic cytoskeletons.
  Curr Opin Cell Biol, 16, 24-31.  
12644989 A.Schlosser, B.Klockow, D.J.Manstein, and W.D.Lehmann (2003).
Analysis of post-translational modification and characterization of the domain structure of dynamin A from Dictyostelium discoideum.
  J Mass Spectrom, 38, 277-282.  
12581669 C.Herrmann (2003).
Ras-effector interactions: after one decade.
  Curr Opin Struct Biol, 13, 122-129.  
12642673 H.Gao, D.Kadirjan-Kalbach, J.E.Froehlich, and K.W.Osteryoung (2003).
ARC5, a cytosolic dynamin-like protein from plants, is part of the chloroplast division machinery.
  Proc Natl Acad Sci U S A, 100, 4328-4333.  
14502270 T.F.Reubold, S.Eschenburg, A.Becker, F.J.Kull, and D.J.Manstein (2003).
A structural model for actin-induced nucleotide release in myosin.
  Nat Struct Biol, 10, 826-830.
PDB code: 1q5g
11823417 B.Klockow, W.Tichelaar, D.R.Madden, H.H.Niemann, T.Akiba, K.Hirose, and D.J.Manstein (2002).
The dynamin A ring complex: molecular organization and nucleotide-dependent conformational changes.
  EMBO J, 21, 240-250.  
11847228 G.Kochs, M.Haener, U.Aebi, and O.Haller (2002).
Self-assembly of human MxA GTPase into highly ordered dynamin-like oligomers.
  J Biol Chem, 277, 14172-14176.  
12011079 S.Ahn, J.Kim, C.L.Lucaveche, M.C.Reedy, L.M.Luttrell, R.J.Lefkowitz, and Y.Daaka (2002).
Src-dependent tyrosine phosphorylation regulates dynamin self-assembly and ligand-induced endocytosis of the epidermal growth factor receptor.
  J Biol Chem, 277, 26642-26651.  
12383797 S.Sever (2002).
Dynamin and endocytosis.
  Curr Opin Cell Biol, 14, 463-467.  
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.