PDBsum entry 5dfz

Transferase

PDB id: 5dfz

Contents

Protein chains

343 a.a.

783 a.a.

1224 a.a.

113 a.a.

341 a.a.

49 a.a.

PDB id:

5dfz

Name:

Transferase

Title:

Structure of vps34 complex ii from s. Cerevisiae.

Structure:

Vacuolar protein sorting-associated protein 38. Chain: a. Engineered: yes. Phosphatidylinositol 3-kinase vps34. Chain: c. Synonym: ptdins-3-kinase vps34,carboxypeptidase y-deficient protein 15,vacuolar protein sorting-associated protein 34,vacuolar protein- targeting protein 29. Engineered: yes.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: vps38, vpl17, ylr360w, l8039.11. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Gene: vps34, end12, pep15, vpl7, vpt29, ylr240w, l9672.10.

Resolution:

4.40Å R-factor: 0.369 R-free: 0.376

Authors:

K.Rostislavleva,N.Soler,Y.Ohashi,L.Zhang,R.L.Williams

Key ref:

K.Rostislavleva et al. (2015). Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science, 350, aac7365. PubMed id: 26450213 DOI: 10.1126/science.aac7365

Date:

27-Aug-15 Release date: 07-Oct-15

Protein chain

Q05919  (VPS38_YEAST) -  Vacuolar protein sorting-associated protein 38 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 439 a.a.

Struc: 343 a.a.

Protein chain

P22543  (VPS34_YEAST) -  Phosphatidylinositol 3-kinase VPS34 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 875 a.a.

Struc: 783 a.a.

Protein chain

P22219  (VPS15_YEAST) -  Serine/threonine-protein kinase VPS15 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1454 a.a.

Struc: 1224 a.a.

Protein chain

No UniProt id for this chain

Struc: 113 a.a.

Protein chain

Q02948  (BECN1_YEAST) -  Vacuolar protein sorting-associated protein 30 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 557 a.a.

Struc: 341 a.a.

Protein chain

No UniProt id for this chain

Struc: 49 a.a.

Enzyme reactions

• Enzyme class 2: Chain B: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺
• Enzyme class 3: Chain C: E.C.2.7.1.137 - phosphatidylinositol 3-kinase.

Pathway:

• Reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + ATP = a 1,2-diacyl- sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + ADP + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1126/science.aac7365

Science 350:aac7365 (2015)

PubMed id: 26450213

Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes.

K.Rostislavleva, N.Soler, Y.Ohashi, L.Zhang, E.Pardon, J.E.Burke, G.R.Masson, C.Johnson, J.Steyaert, N.T.Ktistakis, R.L.Williams.

ABSTRACT

Phosphatidylinositol 3-kinase Vps34 complexes regulate intracellular membrane trafficking in endocytic sorting, cytokinesis, and autophagy. We present the 4.4 angstrom crystal structure of the 385-kilodalton endosomal complex II (PIK3C3-CII), consisting of Vps34, Vps15 (p150), Vps30/Atg6 (Beclin 1), and Vps38 (UVRAG). The subunits form a Y-shaped complex, centered on the Vps34 C2 domain. Vps34 and Vps15 intertwine in one arm, where the Vps15 kinase domain engages the Vps34 activation loop to regulate its activity. Vps30 and Vps38 form the other arm that brackets the Vps15/Vps34 heterodimer, suggesting a path for complex assembly. We used hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal conformational changes accompanying membrane binding and identify a Vps30 loop that is critical for the ability of complex II to phosphorylate giant liposomes on which complex I is inactive.