3VUH

Crystal structure of a cysteine-deficient mutant M3 in MAP kinase JNK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Seven cysteine-deficient mutants depict the interplay between thermal and chemical stabilities of individual cysteine residues in mitogen-activated protein kinase c-Jun N-terminal kinase 1

Nakaniwa, T.Fukada, H.Inoue, T.Gouda, M.Nakai, R.Kirii, Y.Adachi, M.Tamada, T.Segawa, S.Kuroki, R.Tada, T.Kinoshita, T.

(2012) Biochemistry 51: 8410-8421

  • DOI: 10.1021/bi300918w
  • Primary Citation of Related Structures:  3VUD, 3VUG, 3VUI, 3VUK, 3VUL, 3VUM

  • PubMed Abstract: 
  • Intracellular proteins can have free cysteines that may contribute to their structure, function, and stability; however, free cysteines can lead to chemical instabilities in solution because of oxidation-driven aggregation. The MAP kinase, c-Jun N-te ...

    Intracellular proteins can have free cysteines that may contribute to their structure, function, and stability; however, free cysteines can lead to chemical instabilities in solution because of oxidation-driven aggregation. The MAP kinase, c-Jun N-terminal kinase 1 (JNK1), possesses seven free cysteines and is an important drug target for autoimmune diseases, cancers, and apoptosis-related diseases. To characterize the role of cysteine residues in the structure, function, and stability of JNK1, we prepared and evaluated wild-type JNK1 and seven cysteine-deficient JNK1 proteins. The nonreduced sodium dodecyl sulfate-polyacrylamide gel electrophoresis experiments showed that the chemical stability of JNK1 increased as the number of cysteines decreased. The contribution of each cysteine residue to biological function and thermal stability was highly susceptible to the environment surrounding the particular cysteine mutation. The mutations of solvent-exposed cysteine to serine did not influence biological function and increased the thermal stability. The mutation of the accessible cysteine involved in the hydrophobic pocket did not affect biological function, although a moderate thermal destabilization was observed. Cysteines in the loosely assembled hydrophobic environment moderately contributed to thermal stability, and the mutations of these cysteines had a negligible effect on enzyme activity. The other cysteines are involved in the tightly filled hydrophobic core, and mutation of these residues was found to correlate with thermal stability and enzyme activity. These findings about the role of cysteine residues should allow us to obtain a stable JNK1 and thus promote the discovery of potent JNK1 inhibitors.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 8
A
370Homo sapiensGene Names: MAPK8 (JNK1, PRKM8, SAPK1, SAPK1C)
EC: 2.7.11.24
Find proteins for P45983 (Homo sapiens)
Go to Gene View: MAPK8
Go to UniProtKB:  P45983
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide from C-Jun-amino-terminal kinase-interacting protein 1
F
11Homo sapiensGene Names: MAPK8IP1 (IB1, JIP1, PRKM8IP)
Find proteins for Q9UQF2 (Homo sapiens)
Go to Gene View: MAPK8IP1
Go to UniProtKB:  Q9UQF2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.194 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 169.929α = 90.00
b = 169.929β = 90.00
c = 87.315γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASESphasing
HKL-2000data reduction
ADSCdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release