PDBsum entry: 1fmo

Complex (phosphotransferase/inhibitor)

PDB id: 1fmo

Contents

Protein chains

338 a.a. *

20 a.a. *

Ligands

ADN

Waters ×90

* Residue conservation analysis

PDB id:

1fmo

Name:

Complex (phosphotransferase/inhibitor)

Title:

Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of camp-dependent protein kinase complexed with the peptide inhibitor pki(5-24) and adenosine

Structure:

Camp-dependent protein kinase. Chain: e. Fragment: catalytic subunit. Synonym: capk, pka. Engineered: yes. Heat stable rabbit skeletal muscle inhibitor protein. Chain: i. Fragment: residues 5 - 24.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Organ: skeletal. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.182

Authors:

N.Narayana,S.Cox,S.Shaltiel,S.S.Taylor,N.-H.Xuong

Key ref:

N.Narayana et al. (1997). Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI(5-24) and adenosine. Biochemistry, 36, 4438-4448. PubMed id: 9109651 DOI: 10.1021/bi961947+

Date:

08-Jul-97 Release date: 14-Jan-98

Protein chain

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

Seq: 351 a.a.

Struc: 338 a.a.*

Protein chain

P61926  (IPKA_RABIT) -  cAMP-dependent protein kinase inhibitor alpha

Seq: 76 a.a.

Struc: 20 a.a.

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

Enzyme reactions

• Enzyme class: Chain E: E.C.2.7.11.11 - cAMP-dependent protein kinase.
• Reaction: ATP + a protein = ADP + a phosphoprotein

ATP + protein = ADP (Bound ligand (Het Group name = ADN) matches with 70.00% similarity) + phosphoprotein

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

 Gene Ontology (GO) functional annotation 

• Cellular component: neuromuscular junction (16 terms)
• Biological process: positive regulation of cell cycle arrest (13 terms)
• Biochemical function: nucleotide binding (11 terms)

reference

DOI no: 10.1021/bi961947+

Biochemistry 36:4438-4448 (1997)

PubMed id: 9109651

Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI(5-24) and adenosine.

N.Narayana, S.Cox, S.Shaltiel, S.S.Taylor, N.Xuong.

ABSTRACT

The crystal structure of the hexahistidine-tagged mouse recombinant catalytic subunit (H6-rC) of cAMP-dependent protein kinase (cAPK), complexed with a 20-residue peptide inhibitor from the heat-stable protein kinase inhibitor PKI(5-24) and adenosine, was determined at 2.2 A resolution. Novel crystallization conditions were required to grow the ternary complex crystals. The structure was refined to a final crystallographic R-factor of 18.2% with good stereochemical parameters. The "active" enzyme adopts a "closed" conformation as found in rC:PKI(5-24) [Knighton et al. and packs in a similar manner with the peptide providing a major contact surface. This structure clearly defines the subsites of the unique nucleotide binding site found in the protein kinase family. The adenosine occupies a mostly hydrophobic pocket at the base of the cleft between the two lobes and is completely buried. The missing triphosphate moiety of ATP is filled with a water molecule (Wtr 415) which replaces the gamma-phosphate of ATP. The glycine-rich loop between beta1 and beta2 helps to anchor the phosphates while the ribose ring is buried beneath beta-strand 2. Another ordered water molecule (Wtr 375) is pentacoordinated with polar atoms from adenosine, Leu 49 in beta-strand 1, Glu 127 in the linker strand between the two lobes, Tyr 330, and a third water molecule, Wtr 359. The conserved nucleotide fold can be defined as a lid comprised of beta-strand 1, the glycine-rich loop, and beta-strand 2. The adenine ring is buried beneath beta-strand 1 and the linker strand (120-127) that joins the small and large lobes. The C-terminal tail containing Tyr 330, a segment that lies outside the conserved core, covers this fold and anchors it in a closed conformation. The main-chain atoms of the flexible glycine-rich loop (residues 50-55) in the ATP binding domain have a mean B-factor of 41.4 A2. This loop is quite mobile, in striking contrast to the other conserved loops that converge at the active site cleft. The catalytic loop (residues 166-171) and the Mg2+ positioning loop (residues 184-186) are a stable part of the large lobe and have low B-factors in all structures solved to date. The stability of the glycine-rich loop is highly dependent on the ligands that occupy the active site cleft with maximum stability achieved in the ternary complex containing Mg x ATP and the peptide inhibitor. In this ternary complex the gamma-phosphate is secured between both lobes by hydrogen bonds to the backbone amide of Ser 53 in the glycine-rich loop and the amino group of Lys 168 in the catalytic loop. In the adenosine ternary complex the water molecule replacing the gamma-phosphate hydrogen bonds between Lys 168 and Asp 166 and makes no contact with the small lobe. This glycine-rich loop is thus the most mobile component of the active site cleft, with the tip of the loop being highly sensitive to what occupies the gamma-subsite.