PDBsum entry 2v6y

Hydrolase

PDB id: 2v6y

Contents

Protein chains

75 a.a. *

Ligands

SRT ×2

Waters ×8

* Residue conservation analysis

PDB id:

2v6y

Name:

Hydrolase

Title:

Structure of the mit domain from a s. Solfataricus vps4-like atpase

Structure:

Aaa family atpase, p60 katanin. Chain: a. Fragment: mit domain, residues 1-83. Synonym: vps4-like aaa-atpase. Engineered: yes. Aaa family atpase, p60 katanin. Chain: b. Fragment: mit domain, residues 1-83. Synonym: vps4-like aaa-atpase.

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.253 R-free: 0.277

Authors:

T.Obita,S.Saksena,S.Ghazi-Tabatabai,D.J.Gill,O.Perisic,S.D.Emr, R.L.Williams

Key ref:

T.Obita et al. (2007). Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4. Nature, 449, 735-739. PubMed id: 17928861 DOI: 10.1038/nature06171

Date:

24-Jul-07 Release date: 16-Oct-07

Protein chains

Q97ZJ7  (Q97ZJ7_SULSO) -  AAA family ATPase, p60 katanin from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 372 a.a.

Struc: 75 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.4.6 - vesicle-fusing ATPase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature06171

Nature 449:735-739 (2007)

PubMed id: 17928861

Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4.

T.Obita, S.Saksena, S.Ghazi-Tabatabai, D.J.Gill, O.Perisic, S.D.Emr, R.L.Williams.

ABSTRACT

The AAA+ ATPases are essential for various activities such as membrane trafficking, organelle biogenesis, DNA replication, intracellular locomotion, cytoskeletal remodelling, protein folding and proteolysis. The AAA ATPase Vps4, which is central to endosomal traffic to lysosomes, retroviral budding and cytokinesis, dissociates ESCRT complexes (the endosomal sorting complexes required for transport) from membranes. Here we show that, of the six ESCRT--related subunits in yeast, only Vps2 and Did2 bind the MIT (microtubule interacting and transport) domain of Vps4, and that the carboxy-terminal 30 residues of the subunits are both necessary and sufficient for interaction. We determined the crystal structure of the Vps2 C terminus in a complex with the Vps4 MIT domain, explaining the basis for selective ESCRT-III recognition. MIT helices alpha2 and alpha3 recognize a (D/E)xxLxxRLxxL(K/R) motif, and mutations within this motif cause sorting defects in yeast. Our crystal structure of the amino-terminal domain of an archaeal AAA ATPase of unknown function shows that it is closely related to the MIT domain of Vps4. The archaeal ATPase interacts with an archaeal ESCRT-III-like protein even though these organisms have no endomembrane system, suggesting that the Vps4/ESCRT-III partnership is a relic of a function that pre-dates the divergence of eukaryotes and Archaea.

Selected figure(s)

Figure 1.
Figure 1: Characterization of the Vps4–Vps2 complex. a, GST-tagged MIT domain of yeast Vps4 and full-length Vps4 interact with full-length Vps2. Coomassie-stained SDS–PAGE shows the material bound to the glutathione-Sepharose resin. b, c, Vps2 C-terminal constructs (residues 106–232 in b and residues 120–232 in c) also interact with an untagged MIT domain as detected by band-shift on native PAGE. d, Vps2 C-terminal region (residues 183–232) binds to the FlAsH-tagged Vps4 MIT domain with a K[d] of 28 M. e, Structure of the complex between Vps2 (cyan) and the Vps4 MIT domain (yellow). f, Interactions between Vps2 C and MIT domain. g, The distinctive three-corners-of-a-square appearance of the three-helix MIT bundle. h–j, Enlarged central (i) and peripheral Vps2 helix C specificity determinants (N-terminal and C-terminal regions are shown in h and j, respectively).

Figure 3.
Figure 3: MIT-interacting motifs in Vps2 and Did2 are important for function in vivo. a, In wild-type cells, GFP-tagged carboxypeptidase-S accumulates in the vacuolar lumen (FM4-64 preferentially labels the limiting membrane of the vacuole). A single mutation at position 0 of the Vps2 MIM (R224D) impairs sorting, and the GFP–CPS accumulates in the limiting membrane of the vacuole. A double mutation of the Vps2 MIM (L228D/K229D) causes GFP–CPS accumulation in a class E compartment. b, Both a single mutation at position 0 of the Did2 MIM (R198D) and a double mutation (L199D/L202D) impair sorting of GFP–CPS, which accumulates in the limiting membrane of the vacuole.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 449, 735-739) copyright 2007.

Figures were selected by an automated process.