PDBsum entry 2hw6

Transferase

PDB id: 2hw6

Contents

Protein chain

242 a.a. *

Ligands

SO4 ×2

Waters ×138

* Residue conservation analysis

PDB id:

2hw6

Name:

Transferase

Title:

Crystal structure of mnk1 catalytic domain

Structure:

Map kinase-interacting serine/threonine-protein kinase 1. Chain: a, b. Fragment: mnk1-kr. Synonym: map kinase signal-integrating kinase 1, mnk1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: mknk1, mnk1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.209 R-free: 0.257

Authors:

R.Jauch,M.C.Wahl

Key ref:

R.Jauch et al. (2006). Mitogen-activated protein kinases interacting kinases are autoinhibited by a reprogrammed activation segment. EMBO J, 25, 4020-4032. PubMed id: 16917500 DOI: 10.1038/sj.emboj.7601285

Date:

01-Aug-06 Release date: 29-Aug-06

Protein chains

Q9BUB5  (MKNK1_HUMAN) -  MAP kinase-interacting serine/threonine-protein kinase 1 from Homo sapiens

Seq: 465 a.a.

Struc: 242 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.11.1 - non-specific serine/threonine 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: 10.1038/sj.emboj.7601285

EMBO J 25:4020-4032 (2006)

PubMed id: 16917500

Mitogen-activated protein kinases interacting kinases are autoinhibited by a reprogrammed activation segment.

R.Jauch, M.K.Cho, S.Jäkel, C.Netter, K.Schreiter, B.Aicher, M.Zweckstetter, H.Jäckle, M.C.Wahl.

ABSTRACT

Autoinhibition is a recurring mode of protein kinase regulation and can be based on diverse molecular mechanisms. Here, we show by crystal structure analysis, nuclear magnetic resonance (NMR)-based nucleotide affinity studies and rational mutagenesis that nonphosphorylated mitogen-activated protein (MAP) kinases interacting kinase (Mnk) 1 is autoinhibited by conversion of the activation segment into an autoinhibitory module. In a Mnk1 crystal structure, the activation segment is repositioned via a Mnk-specific sequence insertion at the N-terminal lobe with the following consequences: (i) the peptide substrate binding site is deconstructed, (ii) the interlobal cleft is narrowed, (iii) an essential Lys-Glu pair is disrupted and (iv) the magnesium-binding loop is locked into an ATP-competitive conformation. Consistently, deletion of the Mnk-specific insertion or removal of a conserved phenylalanine side chain, which induces a blockade of the ATP pocket, increase the ATP affinity of Mnk1. Structural rearrangements required for the activation of Mnks are apparent from the cocrystal structure of a Mnk2 D228G -staurosporine complex and can be modeled on the basis of crystal packing interactions. Our data suggest a novel regulatory mechanism specific for the Mnk subfamily.

Selected figure(s)

Figure 3.
Figure 3 Autoinhibitory conformation of the activation segment. (A) Ribbon plot of Mnk1-KR. A region corresponding to helix EF and the EF/ F loop traverses the interlobal cleft from the N- to the C-terminal lobe (direction: green arrow). Phe230 (ball-and-stick) of the Mnk-specific insertion I2 in the activation segment occupies the DFG/D-in pocket, thereby pushing Phe192 (ball-and-stick) of the DFD motif into the ATP-binding pocket. (B) Ribbon plot of c-KIT (Mol et al, 2004b) (PDB ID 1T45). The autoinhibitory JM domain is shown in red. It crosses the interlobal cleft from the N- to the C-terminal lobe (red arrow). Trp557 (ball-and-stick) of the JM domain is mechanistically analogous to Phe230 in Mnk1-KR. The activation segment of c-KIT is fully visible in contrast to Mnk1-KR. (C) Close-up stereo ribbon plot showing the activation segment of Mnk1-KR folding back across the interlobal cleft and lining up with helix C. The activation segment and interacting residues are shown in ball-and-stick. Hydrogen bonds and salt bridges that tether the activation segment are shown as dashed lines. Two Arg residues of helix C and two interacting Glu residues of the activation segment are labeled. The molecule has been rotated 45° about the horizontal axis (top to back) compared to Figure 1A.

Figure 4.
Figure 4 ATP binding and DFG/D pockets. Stereo diagrams depicting details of the ATP and DFG/D pockets. Critical residues are labeled. Hydrogen bonds and ionic interactions are depicted by dashed lines. (A) Mnk1-KR with an ionic interaction network involving the Asp residues of the DFD motif. The conserved Lys–Glu ion pair is broken. The final 2F[o]-F[c] electron density (gray; contoured at the 1 level) is shown covering selected residues. (B) Mnk2-KR (Jauch et al, 2005) (PDB-ID 2AC3) in which the DFD-out conformation is retained, although the activation segment has been detached from the N-terminal lobe. No clear interaction involving the Asp residues of the DFD motif can be discerned. (C) DAPK1-Mn^2+–AMPPNP complex (Tereshko et al, 2001) (PDB ID 1IG1). The AMPPNP is shown in ball-and-stick (carbon—brown; phosphorus—pink; Mn^2+—black sphere; water—blue spheres). (D) Mnk2–KR^D228G–staurosporine complex. Staurosporine is shown in ball-and-stick (carbon—brown). Note the complete reversal of the DFD-out to the DFD-in conformation upon staurosporine binding (compare to panel B). The final 2F[o]–F[c] electron density (gray; contoured at the 1 level) is shown covering staurosporine and selected residues.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 4020-4032) copyright 2006.

Figures were selected by an automated process.