PDBsum entry 1j3h

Transferase

PDB id: 1j3h

Contents

Protein chains

332 a.a. *

Ligands

MPD ×2

* Residue conservation analysis

PDB id:

1j3h

Name:

Transferase

Title:

Crystal structure of apoenzyme camp-dependent protein kinase catalytic subunit

Structure:

Camp-dependent protein kinase, alpha-catalytic subunit. Chain: a, b. Synonym: pkac-alpha. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.90Å R-factor: 0.257 R-free: 0.291

Authors:

P.Akamine,Madhusudan,J.Wu,N.H.Xuong,L.F.Ten Eyck,S.S.Taylor

Key ref:

P.Akamine et al. (2003). Dynamic features of cAMP-dependent protein kinase revealed by apoenzyme crystal structure. J Mol Biol, 327, 159-171. PubMed id: 12614615 DOI: 10.1016/S0022-2836(02)01446-8

Date:

31-Jan-03 Release date: 04-Mar-03

Protein chains

P05132  (KAPCA_MOUSE) -  cAMP-dependent protein kinase catalytic subunit alpha from Mus musculus

Seq: 351 a.a.

Struc: 332 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.7.11.11 - cAMP-dependent 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⁺

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

reference

DOI no: 10.1016/S0022-2836(02)01446-8

J Mol Biol 327:159-171 (2003)

PubMed id: 12614615

Dynamic features of cAMP-dependent protein kinase revealed by apoenzyme crystal structure.

P.Akamine, Madhusudan, J.Wu, N.H.Xuong, L.F.Ten Eyck, S.S.Taylor.

ABSTRACT

To better understand the mechanism of ligand binding and ligand-induced conformational change, the crystal structure of apoenzyme catalytic (C) subunit of adenosine-3',5'-cyclic monophosphate (cAMP)-dependent protein kinase (PKA) was solved. The apoenzyme structure (Apo) provides a snapshot of the enzyme in the first step of the catalytic cycle, and in this unliganded form the PKA C subunit adopts an open conformation. A hydrophobic junction is formed by residues from the small and large lobes that come into close contact. This "greasy" patch may lubricate the shearing motion associated with domain rotation, and the opening and closing of the active-site cleft. Although Apo appears to be quite dynamic, many important residues for MgATP binding and phosphoryl transfer in the active site are preformed. Residues around the adenine ring of ATP and residues involved in phosphoryl transfer from the large lobe are mostly preformed, whereas residues involved in ribose binding and in the Gly-rich loop are not. Prior to ligand binding, Lys72 and the C-terminal tail, two important ATP-binding elements are also disordered. The surface created in the active site is contoured to bind ATP, but not GTP, and appears to be held in place by a stable hydrophobic core, which includes helices C, E, and F, and beta strand 6. This core seems to provide a network for communicating from the active site, where nucleotide binds, to the peripheral peptide-binding F-to-G helix loop, exemplified by Phe239. Two potential lines of communication are the D helix and the F helix. The conserved Trp222-Phe238 network, which lies adjacent to the F-to-G helix loop, suggests that this network would exist in other protein kinases and may be a conserved means of communicating ATP binding from the active site to the distal peptide-binding ledge.

Selected figure(s)

Figure 1.
Figure 1. (A) ApoA and ApoB superimposed. The two molecules in the asymmetric unit are superimposed to show that they differ in overall domain rotation. ApoA is black and ApoB is gold. Broken lines are distances of representative areas of the small lobe. The distance between the Ser53 C^a atoms, in the Gly-rich loop, is 1.9 Å. The distance between the C^a atoms of Ser339 is 3.4 Å. An MPD molecule and a covalently attached b-ME group were seen in both structures. The ApoA MPD and b-ME modified Cys199 are pink. Residues 128-300 were superimposed. (B) The F[o] -F[c] omit map of Cys199 and the covalently attached b-ME, contoured at 3s. Oxygen, red; nitrogen, blue; carbon, gray; sulfur, green.

Figure 2.
Figure 2. (A) Closed conformation and ApoA. Superposition of ApoA (black) and C:AlF:SP20 (green),[9] in the open and closed conformations, respectively. Broken lines show the distances of two representative parts of the small lobe; the Gly-rich loop (Ser53 C^a) and the C-terminal tail (Ser339 C^a). Residues 128-300 were superimposed. (B) Intralobe hydrophobic contacts. The hydrophobic patch between the small and large lobes, which may provide the "grease" for the shearing motion associated with domain rotation, is shown. Glu91, a conserved residue in the C helix (C), which is important for orienting the phosphate groups of ATP during phosphoryl transfer, is preformed and is within hydrogen-bonding distance from the amide hydrogen atom of Phe185 in the large lobe. From the small lobe (gold ribbon) are residues Glu91, Ile94, Val98, Phe100, Phe102, Leu103, and Val104 (side-chains, blue). From the large lobe, the residues shown are Thr153, Tyr156, Leu162, Tyr179, Gln181, and Phe185 (side-chains, pink). Residues that come into close contact are Ile94-Leu162, Phe185; Val98, Phe100 and Leu103-Tyr156, Leu103-Phe185, and Val104-Gln181. Other hydrogen bonding pairs are: Asn99 amide group to Tyr156 hydroxyl group, and Val104 amide hydrogen atom to Val182 carbonyl oxygen atom. The gray ribbon represents the E helix (E) and the black ribbon includes the Mg-positioning loop (Mg), both from the large lobe. Helix A (A) is shown, since Phe18, Ala22, and Phe26 contribute, peripherally.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 159-171) copyright 2003.

Figures were selected by an automated process.