PDBsum entry 4qfg

Signaling protein/inhibitor

PDB id: 4qfg

Contents

Protein chains

366 a.a.

161 a.a.

287 a.a.

Ligands

STU

SO4 ×3

AMP

Metals

_CL ×3

PDB id:

4qfg

Name:

Signaling protein/inhibitor

Title:

Structure of ampk in complex with staurosporine inhibitor and in the absence of a synthetic activator

Structure:

5'-amp-activated protein kinase catalytic subunit alpha-1. Chain: a. Fragment: ampk alpha1. Synonym: ampk subunit alpha-1, acetyl-coa carboxylase kinase, acaca kinase, hydroxymethylglutaryl-coa reductase kinase, hmgcr kinase, tau-protein kinase prkaa1. Ec: 2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26. Engineered: yes. Mutation: yes.

Source:

Rattus norvegicus. Brown rat,rat,rats. Organism_taxid: 10116. Gene: ampk1, prkaa1, prkaa1 ampk1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: prkab1. Gene: prkag1. Expression_system_taxid: 562

Resolution:

3.46Å R-factor: 0.224 R-free: 0.267

Authors:

M.F.Calabrese,R.G.Kurumbail

Key ref:

M.F.Calabrese et al. (2014). Structural basis for AMPK activation: natural and synthetic ligands regulate kinase activity from opposite poles by different molecular mechanisms. Structure, 22, 1161-1172. PubMed id: 25066137 DOI: 10.1016/j.str.2014.06.009

Date:

20-May-14 Release date: 06-Aug-14

Protein chain

P54645  (AAPK1_RAT) -  5'-AMP-activated protein kinase catalytic subunit alpha-1 from Rattus norvegicus

Seq: 559 a.a.

Struc: 366 a.a.*

Protein chain

P80386  (AAKB1_RAT) -  5'-AMP-activated protein kinase subunit beta-1 from Rattus norvegicus

Seq: 270 a.a.

Struc: 161 a.a.*

Protein chain

P80385  (AAKG1_RAT) -  5'-AMP-activated protein kinase subunit gamma-1 from Rattus norvegicus

Seq: 330 a.a.

Struc: 287 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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: Chain A: E.C.2.7.11.26 - [tau protein] kinase.
• Reaction:
  1. L-seryl-[tau protein] + ATP = O-phospho-L-seryl-[tau protein] + ADP + H⁺
  2. L-threonyl-[tau protein] + ATP = O-phospho-L-threonyl-[tau protein] + ADP + H⁺

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

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

• Enzyme class 3: Chain A: E.C.2.7.11.31 - [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase.
• Reaction: L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase] + ATP = O-phospho-L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase] + ADP + H⁺

L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase] + ATP = O-phospho-L-seryl-[3-hydroxy-3-methylglutaryl-coenzyme A reductase] (Bound ligand (Het Group name = AMP) matches with 85.19% similarity) + 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: 10.1016/j.str.2014.06.009

Structure 22:1161-1172 (2014)

PubMed id: 25066137

Structural basis for AMPK activation: natural and synthetic ligands regulate kinase activity from opposite poles by different molecular mechanisms.

M.F.Calabrese, F.Rajamohan, M.S.Harris, N.L.Caspers, R.Magyar, J.M.Withka, H.Wang, K.A.Borzilleri, P.V.Sahasrabudhe, L.R.Hoth, K.F.Geoghegan, S.Han, J.Brown, T.A.Subashi, A.R.Reyes, R.K.Frisbie, J.Ward, R.A.Miller, J.A.Landro, A.T.Londregan, P.A.Carpino, S.Cabral, A.C.Smith, E.L.Conn, K.O.Cameron, X.Qiu, R.G.Kurumbail.

ABSTRACT

AMP-activated protein kinase (AMPK) is a principal metabolic regulator affecting growth and response to cellular stress. Comprised of catalytic and regulatory subunits, each present in multiple forms, AMPK is best described as a family of related enzymes. In recent years, AMPK has emerged as a desirable target for modulation of numerous diseases, yet clinical therapies remain elusive. Challenges result, in part, from an incomplete understanding of the structure and function of full-length heterotrimeric complexes. In this work, we provide the full-length structure of the widely expressed α1β1γ1 isoform of mammalian AMPK, along with detailed kinetic and biophysical characterization. We characterize binding of the broadly studied synthetic activator A769662 and its analogs. Our studies follow on the heels of the recent disclosure of the α2β1γ1 structure and provide insight into the distinct molecular mechanisms of AMPK regulation by AMP and A769662.