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PDBsum entry 1jlu
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Transferase/transferase inhibitor
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PDB id
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1jlu
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Camp-Dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer.
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Authors
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Madhusudan,
E.A.Trafny,
N.H.Xuong,
J.A.Adams,
L.F.Ten eyck,
S.S.Taylor,
J.M.Sowadski.
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Ref.
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Protein Sci, 1994,
3,
176-187.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1994,
3,
176-187)
copyright 1994.
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Secondary reference #1
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Title
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2.0 a refined crystal structure of the catalytic subunit of camp-Dependent protein kinase complexed with a peptide inhibitor and detergent.
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Authors
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D.R.Knighton,
S.M.Bell,
J.Zheng,
L.F.Ten eyck,
N.H.Xuong,
S.S.Taylor,
J.M.Sowadski.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1993,
49,
357-361.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. C:PKI(5-24) C
a backbone trace. The PKI(5-24) peptide inhibitor is shown in red. The MEGA-8 detergent, modeled as n-octane, is shown
in blue in the lower left. In green is the superimposed C
a trace of the superseded 2.7 ,/k 1CPK model for residues 54-67 and 307-341.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #2
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Title
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2.2 a refined crystal structure of the catalytic subunit of camp-Dependent protein kinase complexed with mnatp and a peptide inhibitor.
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Authors
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J.Zheng,
E.A.Trafny,
D.R.Knighton,
N.H.Xuong,
S.S.Taylor,
L.F.Ten eyck,
J.M.Sowadski.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1993,
49,
362-365.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. Environment of conserved amino acis surrounding the site of phosphotransfer. For this diagram a serine (shown in red) was modeled into the
P site so that distances between the "y-phosphate and a protein substrate could be estimated. The primary metal site, OM382, is coordinated by the
invariant Asp184, as well as two water molecules as indicated above. The secondary inhibitory metal site, OM383, is coordiated by the invariant
Asnl7, by invariant Asp184, as well as by one water molecule. Asp14, therefore, is shared by both metal sites in this inhibited complex.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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