PDBsum entry 3tdh

Transferase

PDB id: 3tdh

Contents

Protein chains

139 a.a.

104 a.a.

316 a.a.

Ligands

AMP

Waters ×168

PDB id:

3tdh

Name:

Transferase

Title:

Structure of the regulatory fragment of sccharomyces cerevisiae ampk in complex with amp

Structure:

Carbon catabolite-derepressing protein kinase. Chain: a. Engineered: yes. Snf1 protein kinase subunit beta-2. Chain: b. Synonym: protein spm2, snf1-interacting protein 2. Engineered: yes. Nuclear protein snf4. Chain: c.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: snf1, cat1, ccr1, glc2, pas14, ydr477w, d8035.20. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: sip2, spm2, ygl208w, g1155. Gene: snf4, cat3, ygl115w.

Resolution:

2.30Å R-factor: 0.250 R-free: 0.290

Authors:

F.V.Mayer,R.Heath,E.Underwood,M.J.Sanders,D.Carmena,R.Mccartney, F.C.Leiper,B.Xiao,C.Jing,P.A.Walker,L.F.Haire,R.Ogrodowicz, S.R.Martin,M.C.Schmidt,S.J.Gamblin,D.Carling

Key ref:

F.V.Mayer et al. (2011). ADP regulates SNF1, the Saccharomyces cerevisiae homolog of AMP-activated protein kinase. Cell Metab, 14, 707-714. PubMed id: 22019086

Date:

11-Aug-11 Release date: 09-Nov-11

Protein chain

P06782  (SNF1_YEAST) -  Carbon catabolite-derepressing protein kinase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 633 a.a.

Struc: 139 a.a.

Protein chain

P34164  (SIP2_YEAST) -  SNF1 protein kinase subunit beta-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 415 a.a.

Struc: 104 a.a.*

Protein chain

P12904  (AAKG_YEAST) -  5'-AMP-activated protein kinase subunit gamma from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 322 a.a.

Struc: 316 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: Chain A: 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⁺

L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] (Bound ligand (Het Group name = AMP) matches with 85.19% similarity) + ADP + H(+)

L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] (Bound ligand (Het Group name = AMP) matches with 85.19% similarity) + ADP + H(+)

• Enzyme class 2: Chains B, C: E.C.?

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

Cell Metab 14:707-714 (2011)

PubMed id: 22019086

ADP regulates SNF1, the Saccharomyces cerevisiae homolog of AMP-activated protein kinase.

F.V.Mayer, R.Heath, E.Underwood, M.J.Sanders, D.Carmena, R.R.McCartney, F.C.Leiper, B.Xiao, C.Jing, P.A.Walker, L.F.Haire, R.Ogrodowicz, S.R.Martin, M.C.Schmidt, S.J.Gamblin, D.Carling.

ABSTRACT

The SNF1 protein kinase complex plays an essential role in regulating gene expression in response to the level of extracellular glucose in budding yeast. SNF1 shares structural and functional similarities with mammalian AMP-activated protein kinase. Both kinases are activated by phosphorylation on a threonine residue within the activation loop segment of the catalytic subunit. Here we show that ADP is the long-sought metabolite that activates SNF1 in response to glucose limitation by protecting the enzyme against dephosphorylation by Glc7, its physiologically relevant protein phosphatase. We also show that the regulatory subunit of SNF1 has two ADP binding sites. The tighter site binds AMP, ADP, and ATP competitively with NADH, whereas the weaker site does not bind NADH, but is responsible for mediating the protective effect of ADP on dephosphorylation. Mutagenesis experiments suggest that the general mechanism by which ADP protects against dephosphorylation is strongly conserved between SNF1 and AMPK.