PDBsum entry 1jlu

Transferase/transferase inhibitor

PDB id: 1jlu

Contents

Protein chains

339 a.a. *

20 a.a. *

Ligands

OCT

Waters ×116

* Residue conservation analysis

PDB id:

1jlu

Name:

Transferase/transferase inhibitor

Title:

Crystal structure of the catalytic subunit of camp-dependent protein kinase complexed with a phosphorylated substrate peptide and detergent

Structure:

Amp-dependent protein kinase, alpha-catalytic subunit. Chain: e. Synonym: pka c-alpha. Engineered: yes. Camp-dependent protein kinase inhibitor, muscle/brain form. Chain: s. Fragment: residues 5-24. Synonym: pki-alpha. Engineered: yes.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the peptide is naturally found in mus musculus (mouse).

Biol. unit:

Dimer (from PQS)

Resolution:

2.25Å R-factor: 0.181

Authors:

Madhusudan,E.A.Trafny,N.-H.Xuong,J.A.Adams,L.F.Ten Eyck,S.S.Taylor, J.M.Sowadski

Key ref:

Madhusudan et al. (1994). cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer. Protein Sci, 3, 176-187. PubMed id: 8003955 DOI: 10.1002/pro.5560030203

Date:

16-Jul-01 Release date: 01-Aug-01

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 E: 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: 10.1002/pro.5560030203

Protein Sci 3:176-187 (1994)

PubMed id: 8003955

cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer.

Madhusudan, E.A.Trafny, N.H.Xuong, J.A.Adams, L.F.Ten Eyck, S.S.Taylor, J.M.Sowadski.

ABSTRACT

The crystal structure of ternary and binary substrate complexes of the catalytic subunit of cAMP-dependent protein kinase has been refined at 2.2 and 2.25 A resolution, respectively. The ternary complex contains ADP and a 20-residue substrate peptide, whereas the binary complex contains the phosphorylated substrate peptide. These 2 structures were refined to crystallographic R-factors of 17.5 and 18.1%, respectively. In the ternary complex, the hydroxyl oxygen OG of the serine at the P-site is 2.7 A from the OD1 atom of Asp 166. This is the first crystallographic evidence showing the direct interaction of this invariant carboxylate with a peptide substrate, and supports the predicted role of Asp 166 as a catalytic base and as an agent to position the serine -OH for nucleophilic attack. A comparison of the substrate and inhibitor ternary complexes places the hydroxyl oxygen of the serine 2.7 A from the gamma-phosphate of ATP and supports a direct in-line mechanism for phosphotransfer. In the binary complex, the phosphate on the Ser interacts directly with the epsilon N of Lys 168, another conserved residue. In the ternary complex containing ATP and the inhibitor peptide, Lys 168 interacts electrostatically with the gamma-phosphate of ATP (Zheng J, Knighton DR, Ten Eyck LF, Karlsson R, Xuong NH, Taylor SS, Sowadski JM, 1993, Biochemistry 32:2154-2161). Thus, Lys 168 remains closely associated with the phosphate in both complexes. A comparison of this binary complex structure with the recently solved structure of the ternary complex containing ATP and inhibitor peptide also reveals that the phosphate atom traverses a distance of about 1.5 A following nucleophilic attack by serine and transfer to the peptide. No major conformational changes of active site residues are seen when the substrate and product complexes are compared, although the binary complex with the phosphopeptide reveals localized changes in conformation in the region corresponding to the glycine-rich loop. The high B-factors for this loop support the conclusion that this structural motif is a highly mobile segment of the protein.

Selected figure(s)

Figure 5.
Fig. 5. Diagramofesentialresiduesthatcontribtetonucleotidebindingndcatalysis. A: Inhibitorternarycomplex. Dis- tancesaretakenfromtheternarycomplexof C:IPZO:ATP (Zhengetal.,1993~).Thecrystalsweresoaked in MnZ*, andboth theinhibitorandtheactivatingmetalsareshown (++) (Zhengetal., 1993~).The activating metal bridges the p- andy-phosphates, whereastheinhibitorymetalbridgesthe Y- andy-phospates.Thearrowbridgesthemethylsidechain f theP-siteAlaand they-phosphate of ATP. B: Substrateternarycomplex. C: Phosphorylatedsubstratebinarycomplex.

Figure 8.
ig. 8. Stereoviewshowingthesuperimposition f inaryandternarycomplexesandhigh- lighting localized chagesin the glycine-rich loop. Overallcomparison of the a-carbon back- bone of the pper omain(residues 15-127) of the ternary complexwith MnATP (red),thebi- nary withproductpeptide (blue), and the mammalianC-subunitbinarycomplexwih di-iodinated Tyr 7 PKI(5-24) (green). In hese 3 structures,thelargelobesaresuperimposedand are omitted from thedrawing, as theysho no major conformational changes.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1994, 3, 176-187) copyright 1994.

Figures were selected by an automated process.