PDBsum entry 1l3r

Transferase

PDB id: 1l3r

Contents

Protein chains

341 a.a. *

20 a.a. *

Ligands

ADP-AF3

MPD

Metals

_MG ×2

Waters ×233

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of a transition state mimic of the catalytic subunit of camp-Dependent protein kinase.

Authors

Madhusudan, P.Akamine, N.H.Xuong, S.S.Taylor.

Ref.

Nat Struct Biol, 2002, 9, 273-277. [DOI no: 10.1038/nsb780]

PubMed id

11896404

Abstract

To understand the molecular mechanism underlying phosphoryl transfer of cAMP-dependent protein kinase, the structure of the catalytic subunit in complex with ADP, aluminum fluoride, Mg2+ ions and a substrate peptide was determined at 2.0 A resolution. Aluminum fluoride was modeled as AlF3 in a planar geometry; it is positioned 2.3 A from both the donor oxygen of ADP and the hydroxyl group of the recipient Ser residue. In this configuration, the aluminum atom forms a trigonal bipyramidal coordination with the oxygen atoms of the donor and recipient groups at the apical positions. This arrangement suggests that aluminum fluoride mimics the transition state and provides the first direct structural evidence for the in-line mechanism of phosphoryl transfer in a protein kinase.

Figure 1.
Figure 1. Overall view of the Mg[2]ADP -SP20 -AlF[3] complex of the catalytic subunit (cAPK) with the difference density at the position of AlF[3]. a, The disordered region of the catalytic subunit consisting of residues 5 -13 is indicated by dashes. SP20 and Mg2+ ions are displayed in yellow and red, respectively, and ADP and AlF[3] are shown in green. The Gly-rich loop is colored in magenta, and black spheres indicate the three phosphorylation sites observed in the structure. The MPD molecule is displayed in cyan. This figure was generated using MOLSCRIPT33. b, Stereo view of the annealed F[o] - F[c] omit map contoured at 6.0 . This figure was generated from BOBSCRIPT33, 34. Dashed lines indicate the aluminum (Al) coordination with the -phosphate of ADP and the hydroxyl group of Ser from the SP20.

Figure 3.
Figure 3. Schematic representation depicting the detailed interactions of aluminum fluoride with Mg[2]ADP, active site residues of the catalytic subunit, water molecules and the phosphorylation site Ser from SP20. Mg2+ ions and water molecules are indicated in large and small spheres, respectively. Residues displayed in ball-and-stick representation exhibit the exact conformation and relative orientation as observed in the crystal structure; however, they have been displaced with respect to one another for clarity.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 273-277) copyright 2002.

Secondary reference #1

Title

2.0 a refined crystal structure of the catalytic subunit of camp-Dependent protein kinase complexed with a peptide inhibitor and detergent.

Authors

D.R.Knighton, S.M.Bell, J.Zheng, L.F.Ten eyck, N.H.Xuong, S.S.Taylor, J.M.Sowadski.

Ref.

Acta Crystallogr D Biol Crystallogr, 1993, 49, 357-361. [DOI no: 10.1107/S0907444993000502]

PubMed id

15299526

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.

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #2

Title

2.2 a refined crystal structure of the catalytic subunit of camp-Dependent protein kinase complexed with mnatp and a peptide inhibitor.

Authors

J.Zheng, E.A.Trafny, D.R.Knighton, N.H.Xuong, S.S.Taylor, L.F.Ten eyck, J.M.Sowadski.

Ref.

Acta Crystallogr D Biol Crystallogr, 1993, 49, 362-365. [DOI no: 10.1107/S0907444993000423]

PubMed id

15299527

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.

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #3

Title

Camp-Dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer.

Authors

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

Ref.

Protein Sci, 1994, 3, 176-187. [DOI no: 10.1002/pro.5560030203]

PubMed id

8003955

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 reproduced from the cited reference which is an Open Access publication published by the Protein Society