Structural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125

In the paper

“The K d values for pepJIP1 to bind to wild type, R127A, and E329A were found to be 0.42 7 0.13, 6.4 7 2.2, and 9.1 7 3.4 m M, respectively”

In the paper

“The peptide docks to the docking groove of JNK1, a surface of the Cterminal domain covering a 2, a 3, a 13, and b 8, which is away from the ATP pocket or substrate recognition site”

In the paper

“In this structure, it is found that the docking site of the scaffolding protein also binds at the same docking grooves of JNK1 as the upstream kinase and the substrate transcription factor do in p38 MAPK (Chang et al , 2002), but with quite different interaction modes.”

What the sources say

• Not checked yetcites Chang et al , 2002 source

In the paper

“Much more residues of the phosphorylation loop of the JNK1 complex are disordered than the JNK3 structure (missing residues 175-187 in JNK1-pepJIP1 and 212-216 in JNK3) although their ordered regions adopt a similar conformation”

In the paper

“The most interesting result of the pepJIP1 binding to JNK1 is the rotation of the N-terminal domain relative to the Cterminal domain by approximately 15 1 , thereby distorting the ATP-binding site and inducing disorder of the phosphorylation loop”

In the paper

“The most striking feature of the present structure is the distortion of the ATP-binding site induced by the interdomain rearrangement upon pepJIP1 binding, providing another mechanism of allosteric inhibition of the kinase activity by interfering with productive binding of ATP.”

In the paper

“The hinge motion is triggered in b 8, which interacts with Leu162 ( f B) by van der Waals contacts, and is propagated to the N-terminal domain via the single loop, which connects b 7 and b 8.”

In the paper

“Fortunately, the small molecule, SP600125, occupied the deepest adenine-binding site only, not expanding to the phosphate-binding site”

In the paper

“The most notable difference is that the f A-Xf B motif of pepJIP1, especially Leu162 ( f B), is shifted by the structural difference between JNK1 and p38 in the region containing the hydrophobic residues critical for the f A-Xf B motif binding. In this region, JNK1 forms a oneturn helix ( a 2), but a two-turn helix in p38.”

In the paper

“in the structure of the JNK1-pepJIP1 complex, the a 1 helix moved too far away for such interactions to occur as a result of the interdomain rearrangement upon pepJIP1 binding, and this loss of interactions released the phosphorylation loop of JNK1pepJIP1 from the N-terminal domain, resulting in the increased disorder of the loop.”

In the paper

“The root-mean-square (r.m.s.) deviations for C a atoms of the Nand C-terminal domain between the structures of JNK1-pepJIP1 and JNK3 are 1.27 and 0.79 A ˚ , respectively. These values show that there is no significant structural difference between the corresponding domains.”

In the paper

“However, the overexpression of either the domain within JIP1 that binds to JNK, or the full-length protein, potently inhibits JNK signaling in the cell (Dickens et al , 1997).”

What the sources say

• Not checked yetcites Dickens et al , 1997 source

In the paper

“JNK-interacting protein-1 (JIP1) was identified as a scaffolding protein of the JNK module in yeast two-hybrid analysis, enhancing the correspondent signaling through the pathway (Whitmarsh et al , 1998).”

What the sources say

• Not checked yetcites Whitmarsh et al , 1998 source
• Not checked yetcites Dickens et al , 1997 source

In the paper

“In the structure, the INK4 inhibitors bind next to the ATP-binding site, opposite where the activating cyclin binds, and thereby not only prevent cyclin binding indirectly but also reduce the affinity of the kinase for ATP by causing extensive allosteric changes in CDK6.”

What the sources say

• Not checked yetcites Brotherton et al , 1998 source
• Not checked yetcites Russo et al , 1998 source

In the paper

“This implies that JNK and p38 may act as chemomechanical energy transducers, using peptide binding energy to generate allosteric conformational changes (Goldsmith, 1996).”

What the sources say

• Not checked yetcites Goldsmith, 1996 source

In the paper

“However, similar but nonidentical docking grooves in each MAPKs appear to be the important determinant of pathway specificity in addition to the variations in sequences of docking sites.”

In the paper

“And the size of the pocket may also be connected with the intrinsic flexibility of the loops around the catalytic cleft in protein kinases, and the diverse modes of the flexibility dependent on each protein kinases could be important determinants of the selectivity of SP600125.”

In the paper

“SP600125 is a reversible ATPcompetitive inhibitor with more than 20-fold selectivity over other kinases including Erk, p38 MAPKs, MKKs, and PKCs.”

What the sources say

• Not checked yetcites Bennett et al , 2001 source

In the paper

“Recently, the structure of JNK3 in complex with SP600125 was reported (PDB entry 1PMV; Scapin et al , 2003).”

What the sources say

• Not checked yetcites Scapin et al , 2003 source

In the paper

“In cells, SP600125 dose-dependently inhibited the phosphorylation of c-jun, the expression of inflammatory genes COX-2, IL2, IHNg , and TNFa , and prevented the activation and differentiation of human CD4 cell.”

What the sources say

• Not checked yetcites Bennett et al , 2001 source

In the paper

“The latest result demonstrates that the JNK specificity of SP600125 is not so excellent and this compound inhibits some protein kinases with similar or greater potency than JNK (Bain et al , 2003).”

What the sources say

• Not checked yetcites Bain et al , 2003 source

In the paper

“This distortion would not eliminate the ATP binding, but it would significantly reduce ATP affinity and may well disorient any bound ATP with respect to the kinase catalysis, and thus inhibit the JNK activity to phosphorylate the substrates.”

In the paper

“the release of the phosphorylation loop, when JNK binds to the JIP1 scaffolding protein, may give a chance for the loop to refold and take an appropriate conformation to be recognized and phosphorylated by MKKs, which are also scaffolded in JIP1, and be ready to recognize the substrates.”

In the paper

“the docking site can be characterized by not only the sequential similarity of the f A-Xf B motifs but also the conformational conservation of the motifs in their structures.”

In the paper

“In in vivo studies in mice, SP600125 inhibited lipopolysaccharide-induced expression of TNFa and prevented anti-CD3-mediated thymocyte apoptosis (Bennett et al , 2001).”

What the sources say

• Not checked yetcites Bennett et al , 2001 source

In the paper

“In other words, the inhibition of the full-length JIP1 in vivo is more complicated than that of pepJIP1, and the structural feature of the inhibition by full-length JIP1 might have significant differences from that of pepJIP1.”

In the paper

“The docking groove of JNK1 is expected to accommodate the docking sites of MKK7 or c-jun as that of p38 does, but there may exist other important determinants than the interaction by Arg156 ( f A 4) of JIP1 for specific recognition of the docking sites of MKK7 or c-jun because this residue is not conserved in the sequential comparison (Figure 1D).”

In the paper

“Phosphorylation of JNK by MKKs and activation of c-jun by JNK also might undergo such an interdomain rearrangement as the JNK1-pepJIP1 complex due to the intrinsic flexibility of the loops around the catalytic cleft.”

In the paper

“These previous studies imply that therapeutic inhibition of JNK has significant potential in inflammatory disease, acute organ failure due to apoptotic cell death, and cancer.”

In the paper

“The fact that the N- and C-terminal domains are linked by only two loops, the loop connecting b 7 and b 8 and the disordered 331-351 loop, implies that the intrinsic flexibility may exist in the kinase, and the inherent structural flexibility may play a central role in its regulation upon JIP1 binding to JNK1.”