PDBsum entry 4ib3

Transferase/peptide

PDB id: 4ib3

Contents

Protein chains

339 a.a.

20 a.a.

Ligands

ADP

Waters ×254

PDB id:

4ib3

Name:

Transferase/peptide

Title:

Structure of camp dependent protein kinase a in complex with adp, phosphorylated peptide psp20, and no metal

Structure:

Camp-dependent protein kinase catalytic subunit alpha. Chain: a. Synonym: pka c-alpha. Engineered: yes. Phosphorylated pseudo-substrate peptide psp20. Chain: s. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: prkaca, pkaca. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Homo sapiens. Human.

Resolution:

2.20Å R-factor: 0.182 R-free: 0.228

Authors:

O.Gerlits,A.Kovalevsky

Key ref:

O.Gerlits et al. (2014). Metal-free cAMP-dependent protein kinase can catalyze phosphoryl transfer. Biochemistry, 53, 3179-3186. PubMed id: 24786636 DOI: 10.1021/bi5000965

Date:

07-Dec-12 Release date: 11-Dec-13

Protein chain

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

Seq: 351 a.a.

Struc: 339 a.a.*

Protein chain

P61925  (IPKA_HUMAN) -  cAMP-dependent protein kinase inhibitor alpha from Homo sapiens

Seq: 76 a.a.

Struc: 20 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain A: 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⁺

L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] (Bound ligand (Het Group name = ADP) corresponds exactly) + ADP + H(+)

L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] (Bound ligand (Het Group name = ADP) corresponds exactly) + ADP + H(+)

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

reference

DOI no: 10.1021/bi5000965

Biochemistry 53:3179-3186 (2014)

PubMed id: 24786636

Metal-free cAMP-dependent protein kinase can catalyze phosphoryl transfer.

O.Gerlits, A.Das, M.M.Keshwani, S.Taylor, M.J.Waltman, P.Langan, W.T.Heller, A.Kovalevsky.

ABSTRACT

X-ray structures of several ternary product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have been determined with no bound metal ions and with Na(+) or K(+) coordinated at two metal-binding sites. The metal-free PKAc and the enzyme with alkali metals were able to facilitate the phosphoryl transfer reaction. In all studied complexes, the ATP and the substrate peptide (SP20) were modified into the products ADP and the phosphorylated peptide. The products of the phosphotransfer reaction were also found when ATP-γS, a nonhydrolyzable ATP analogue, reacted with SP20 in the PKAc active site containing no metals. Single turnover enzyme kinetics measurements utilizing (32)P-labeled ATP confirmed the phosphotransferase activity of the enzyme in the absence of metal ions and in the presence of alkali metals. In addition, the structure of the apo-PKAc binary complex with SP20 suggests that the sequence of binding events may become ordered in a metal-free environment, with SP20 binding first to prime the enzyme for subsequent ATP binding. Comparison of these structures reveals conformational and hydrogen bonding changes that might be important for the mechanism of catalysis.