PDBsum entry 2v8q

Transferase

PDB id: 2v8q

Contents

Protein chains

102 a.a. *

73 a.a. *

304 a.a. *

Ligands

AMP ×3

Waters ×428

* Residue conservation analysis

PDB id:

2v8q

Name:

Transferase

Title:

Crystal structure of the regulatory fragment of mammalian ampk in complexes with amp

Structure:

5'-amp-activated protein kinase catalytic subunit alpha-1. Chain: a. Fragment: residues 396-548. Synonym: amp-activated protein kinase, ampk alpha-1 chain. Engineered: yes. 5'-amp-activated protein kinase subunit beta-2. Chain: b. Fragment: residues 187-272. Synonym: amp-activated protein kinase, ampk beta-2 chain.

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.213 R-free: 0.237

Authors:

B.Xiao,R.Heath,P.Saiu,F.C.Leiper,P.Leone,C.Jing,P.A.Walker,L.Haire, J.F.Eccleston,C.T.Davis,S.R.Martin,D.Carling,S.J.Gamblin

Key ref:

B.Xiao et al. (2007). Structural basis for AMP binding to mammalian AMP-activated protein kinase. Nature, 449, 496-500. PubMed id: 17851531 DOI: 10.1038/nature06161

Date:

13-Aug-07 Release date: 25-Sep-07

Protein chain

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

Seq: 559 a.a.

Struc: 102 a.a.*

Protein chain

O43741  (AAKB2_HUMAN) -  5'-AMP-activated protein kinase subunit beta-2 from Homo sapiens

Seq: 272 a.a.

Struc: 73 a.a.

Protein chain

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

Seq: 330 a.a.

Struc: 304 a.a.

* PDB and UniProt seqs differ at 3 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: 10.1038/nature06161

Nature 449:496-500 (2007)

PubMed id: 17851531

Structural basis for AMP binding to mammalian AMP-activated protein kinase.

B.Xiao, R.Heath, P.Saiu, F.C.Leiper, P.Leone, C.Jing, P.A.Walker, L.Haire, J.F.Eccleston, C.T.Davis, S.R.Martin, D.Carling, S.J.Gamblin.

ABSTRACT

AMP-activated protein kinase (AMPK) regulates cellular metabolism in response to the availability of energy and is therefore a target for type II diabetes treatment. It senses changes in the ratio of AMP/ATP by binding both species in a competitive manner. Thus, increases in the concentration of AMP activate AMPK resulting in the phosphorylation and differential regulation of a series of downstream targets that control anabolic and catabolic pathways. We report here the crystal structure of the regulatory fragment of mammalian AMPK in complexes with AMP and ATP. The phosphate groups of AMP/ATP lie in a groove on the surface of the gamma domain, which is lined with basic residues, many of which are associated with disease-causing mutations. Structural and solution studies reveal that two sites on the gamma domain bind either AMP or Mg.ATP, whereas a third site contains a tightly bound AMP that does not exchange. Our binding studies indicate that under physiological conditions AMPK mainly exists in its inactive form in complex with Mg.ATP, which is much more abundant than AMP. Our modelling studies suggest how changes in the concentration of AMP ([AMP]) enhance AMPK activity levels. The structure also suggests a mechanism for propagating AMP/ATP signalling whereby a phosphorylated residue from the alpha and/or beta subunits binds to the gamma subunit in the presence of AMP but not when ATP is bound.

Selected figure(s)

Figure 1.
Figure 1: Structure of mammalian AMPK. a, Diagram representation of the three components of the heterotrimer; the constructs used for crystallization are shown hatched. b, Ribbon representation of the crystallized complex with three bound AMPs in two orthogonal views. The three domains are coloured according to a and the AMP molecules are shown in ball-and-stick representation. For ease of viewing the ends of two loops that are disordered in the structure ( 470–523 and 223–232) are joined-up by a thin black line, also the first 12 residues of that interact with a neighbouring molecule in the crystal lattice are omitted. On the right-hand panel, thin black arrows indicate the position of the approximate two-fold axes relating the four CBS motifs. The subunit comprises Bateman domain 1 (CBS1 + 2) and Bateman domain 2 (CBS3 + 4). The interface between the two CBS motifs of each Bateman domain generates two potential adenyl-binding sites, each being made up from a strand and a helix from each CBS motif—these elements, for the AMP-2 site, are coloured in a lighter shade in b and are shown in more detail in c.

Figure 3.
Figure 3: Front and back views of the three adenyl moieties bound to the bold gamma-domain, shown in surface representation. The surface is coloured according to electrostatic potential (blue, positive; red, negative) and the labelled nucleotides are in ball-and-stick representation, with the magnesium ions shown as yellow spheres. The lower panel represents approximately the same orientation of the molecule shown in the right-hand panel of Fig. 1b, whereas the upper panel is viewed from the back. The left-hand panels show the domain from the AMP complex, whereas the right-hand panels focus on the phosphate-binding groove from the AMP[3] and (Mg ATP)[2]AMP[1] complexes.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 449, 496-500) copyright 2007.

Figures were selected by an automated process.