PDBsum entry 1jx2

Hydrolase

PDB id: 1jx2

Contents

Protein chain

1039 a.a. *

Ligands

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-2 heavy chain,dynamin-a. Chain: a. Fragment: catalytic domain. Synonym: myosin ii heavy chain. Engineered: yes

Source:

Dictyostelium discoideum. Slime mold. Organism_taxid: 44689. Gene: mhca, ddb_g0286355, dyma, ddb_g0277849. Expressed in: dictyostelium discoideum. Expression_system_taxid: 44689.

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

Protein chain

P08799  (MYS2_DICDI) -  Myosin-2 heavy chain from Dictyostelium discoideum

Seq: 2116 a.a.

Struc: 1039 a.a.*

Protein chain

Q94464  (DYNA_DICDI) -  Dynamin-A from Dictyostelium discoideum

Seq: 853 a.a.

Struc: 1039 a.a.*

* PDB and UniProt seqs differ at 274 residue positions (black crosses)

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.