New cAMP-dependent protein kinase structures from UCSD

Daniel R. Knighton dlk at chem.ucsd.edu
Fri Apr 2 08:23:06 EST 1993


Dear cAMP-dependent protein kinase (PKA, cAPK) aficionados,

Because confusion exists about what coordinate sets are available from whom,
I will list here what *UCSD* prerelease coordinate entries are about to become
available by April 2, 1993, from pdb.pdb.bnl.gov:

1ATP (pdb1atp.ent):  2.2-Angstrom refined structure of a recombinant mouse
cAMP-dependent protein kinase catalytic subunit complexed with PKI(5-24)
and MnATP.

1APM (pdb1apm.ent):  2.0-Angstrom refined structure of a recombinant mouse
cAMP-dependent protein kinase catalytic subunit (S139A mutant) complexed
with PKI(5-24) and the detergent octanoyl-N-methyl glucamide (MEGA-8),
which binds in the same place as the mammalian enzyme's N-terminal myristic
acid moiety.

Both of these models have R-factors below 0.19 against all F/sigma>2 data and 
also good geometry, with r.m.s. deviations from ideal bond lengths for both of
0.013 Angstroms, and from ideal bond angles of 2.2 and 2.3 degrees.
The structure factors for these two models are on hold until April, 1994.

One other UCSD entry that has been available by ftp since Dec. 2, 1992, from
the PDB (notice posted here Dec. 4, 1992) and that will still be available,
because it is of crystallized mixed-phosphoform catalytic subunit and has
a model for phospho-Ser 139, is 2CPK (pdb2cpk.ent).  This is still at 2.7
Angstroms and was a 10/92 deposition to correct sequence register errors in
two places in our initial 1991 structure model deposited as 1CPK.  (If you
are still using 1CPK, please discard it immediately and get 1APM for the
backbone and 2CPK only if you have interest in Ser 139.)

Published articles from UCSD that reflect information from our two
high-resolution refinements are the following [two additional
articles are also in the press in Acta Cryst. D49 (1993)]:
"A template for the protein kinase family," S.S. Taylor, et al., Trends in
Biochemical Sciences (TIBS) 18(3), 84-89 (1993).

"Crystal Structure of the Catalytic Subunit of cAMP-Dependent Protein Kinase
Complexed with MgATP and Peptide Inhibitor," J. Zheng, et al., Biochemistry
32(9), 2154-2161 (1993).

I have no information regarding the coordinates of the independently
solved porcine heart catalytic subunit structure complexed with PKI(5-24) and
MnAMPPNP mentioned as having been deposited in the PDB by D. Bossemeyer, et
al., EMBO J. 12(3), 849-859 (1993).  However, the coordinates mentioned by
Dr. E. Abola of the PDB in posts to bionet.xtallography as being newly
available by today from the prerelease directory of pdb.pdb.bnl.gov should
include at least the two UCSD entries I have described.

As before, if you are unable to get any of the UCSD coordinates from the PDB
for whatever reason, I will gladly e-mail any of them to you.

Sincerely yours,

Daniel R. Knighton
dlk at chem.ucsd.edu
FAX: 001-619-622-3299




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