4MYG

MAPK13, active form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.594 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation.

Yurtsever, Z.Scheaffer, S.M.Romero, A.G.Holtzman, M.J.Brett, T.J.

(2015) Acta Crystallogr.,Sect.D 71: 790-799

  • DOI: 10.1107/S1399004715001212

  • PubMed Abstract: 
  • The p38 MAP kinases (p38 MAPKs) represent an important family centrally involved in mediating extracellular signaling. Recent studies indicate that family members such as MAPK13 (p38δ) display a selective cellular and tissue expression and are theref ...

    The p38 MAP kinases (p38 MAPKs) represent an important family centrally involved in mediating extracellular signaling. Recent studies indicate that family members such as MAPK13 (p38δ) display a selective cellular and tissue expression and are therefore involved in specific diseases. Detailed structural studies of all p38 MAPK family members are crucial for the design of specific inhibitors. In order to facilitate such ventures, the structure of MAPK13 was determined in both the inactive (unphosphorylated; MAPK13) and active (dual phosphorylated; MAPK13/pTpY) forms. Here, the first preparation, crystallization and structure determination of MAPK13/pTpY are presented and the structure is compared with the previously reported structure of MAPK13 in order to facilitate studies for structure-based drug design. A comprehensive analysis of inactive versus active structures for the p38 MAPK family is also presented. It is found that MAPK13 undergoes a larger interlobe configurational rearrangement upon activation compared with MAPK14. Surprisingly, the analysis of activated p38 MAPK structures (MAP12/pTpY, MAPK13/pTpY and MAPK14/pTpY) reveals that, despite a high degree of sequence similarity, different side chains are used to coordinate the phosphorylated residues. There are also differences in the rearrangement of the hinge region that occur in MAPK14 compared with MAPK13 which would affect inhibitor binding. A thorough examination of all of the active (phosphorylated) and inactive (unphosphorylated) p38 MAPK family member structures was performed to reveal a common structural basis of activation for the p38 MAP kinase family and to identify structural differences that may be exploited for developing family member-specific inhibitors.


    Organizational Affiliation

    Biochemistry Program, Washington University School of Medicine, St Louis, MO 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 13
A, B
372Homo sapiensMutation(s): 0 
Gene Names: MAPK13 (PRKM13, SAPK4)
EC: 2.7.11.24
Find proteins for O15264 (Homo sapiens)
Go to Gene View: MAPK13
Go to UniProtKB:  O15264
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.594 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 
  • Space Group: P 65
  • Diffraction Data DOI: 
    10.15785/SBGRID/29 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 107.232α = 90.00
b = 107.232β = 90.00
c = 125.531γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
BALBESphasing
HKL-2000data scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references
  • Version 1.2: 2015-04-22
    Type: Database references