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PDBsum entry 3hvc

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Transferase PDB id
3hvc
Jmol
Contents
Protein chain
327 a.a. *
Ligands
GG5 ×2
Waters ×193
* Residue conservation analysis
PDB id:
3hvc
Name: Transferase
Title: Crystal structure of human p38alpha map kinase
Structure: Mitogen-activated protein kinase 14. Chain: a. Synonym: mitogen-activated protein kinase p38 alpha, map kinase p38 alpha, cytokine suppressive anti-inflammatory drug-binding protein, csaid-binding protein, csbp, max- interacting protein 2, map kinase mxi2, sapk2a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: csbp, csbp1, csbp2, cspb1, mapk14, mxi2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.226     R-free:   0.267
Authors: J.J.Perry,J.A.Tainer
Key ref:
J.J.Perry et al. (2009). p38alpha MAP kinase C-terminal domain binding pocket characterized by crystallographic and computational analyses. J Mol Biol, 391, 1. PubMed id: 19501598 DOI: 10.1016/j.jmb.2009.06.005
Date:
15-Jun-09     Release date:   30-Jun-09    
Supersedes: 2p5a
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q16539  (MK14_HUMAN) -  Mitogen-activated protein kinase 14
Seq:
Struc:
360 a.a.
327 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.24  - Mitogen-activated protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
= ADP
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell   8 terms 
  Biological process     intracellular signal transduction   71 terms 
  Biochemical function     nucleotide binding     11 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2009.06.005 J Mol Biol 391:1 (2009)
PubMed id: 19501598  
 
 
p38alpha MAP kinase C-terminal domain binding pocket characterized by crystallographic and computational analyses.
J.J.Perry, R.M.Harris, D.Moiani, A.J.Olson, J.A.Tainer.
 
  ABSTRACT  
 
The mitogen-activated protein (MAP) kinase protein family has a critical role in cellular signaling events, with MAP kinase p38alpha acting in inflammatory processes and being an important drug discovery target. MAP kinase drug design efforts have focused on small-molecule inhibitors of the ATP catalytic site, which exhibit dose-limiting adverse effects. Therefore, characterizing other potential sites that bind substrates, inhibitors, or allosteric effectors is of great interest. Here, we present the crystal structure of human p38alpha MAP kinase, which has a lead compound bound both in the active site and in the lipid-binding site of the C-terminal cap. This C-terminal cap is formed from an extension to the kinase fold, unique to the MAP kinase and cyclin-dependent kinase families and glycogen synthase kinase 3. Binding of this lead, 4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]pyridine, to wild-type p38alpha induces movement of the C-terminal cap region, creating a hydrophobic pocket centered around residue Trp197. Computational analysis of this C-terminal domain pocket indicates notable flexibility for potentially binding different-shaped compounds, including lipids, oxidized arachidonic acid species such as leukotrienes, and small-molecule effectors. Furthermore, our structural results defining the open p38alpha C-lobe pocket provide a detailed framework for the design of novel small molecules with affinities comparable to active-site binders: to bind and potentially modulate the shape and activity of p38alpha in predetermined ways. Moreover, these results and analyses of p38alpha suggest strategies for designing specific binding compounds applicable to other MAP kinases, as well as the cyclin-dependent kinase family and glycogen synthase kinase 3beta that also utilize the C-terminal insert in their interactions.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The molecular structures of (a) 4-FPP and (b) SB203580.
Figure 2.
Fig. 2. The p38α MAP kinase:4-FPP complex crystal structure. (a) The p38α MAP kinase:4-FPP complex structure, with secondary structural elements in green and surface in transparent gray. Two 4-FPP molecules, depicted as spheres, are bound to p38α. One molecule is bound at the active site and is shown in magenta, and the second binds to the C-terminal domain MAP kinase hydrophobic pocket, depicted in salmon. (b) Interactions of 4-FPP in the active-site pocket (the surface of p38α is depicted in transparent gray). 4-FPP forms a 2.7 Å hydrogen bond with the Met109 main-chain nitrogen, and the pyrazol group forms a hydrogen bond with a water molecule that also forms hydrogen bonds with the Asp168 (of the ‘DFG’ loop) and Lys53 side chains (hydrogen bonds are depicted as yellow broken lines, and distances are expressed in angstroms).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 391, 1) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20626350 A.Cuadrado, and A.R.Nebreda (2010).
Mechanisms and functions of p38 MAPK signalling.
  Biochem J, 429, 403-417.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.