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PDBsum entry 1szm

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1szm
Jmol
Contents
Protein chains
320 a.a. *
Ligands
BI4 ×2
Waters ×79
* Residue conservation analysis
PDB id:
1szm
Name: Transferase
Title: Dual binding mode of bisindolylmaleimide 2 to protein kinase a (pka)
Structure: Camp-dependent protein kinase, alpha-catalytic subunit. Chain: a, b. Synonym: pka c-alpha, protein kinase a. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Gene: prkaca. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.50Å     R-factor:   0.234     R-free:   0.289
Authors: M.Gassel,C.B.Breitenlechner,N.Koenig,R.Huber,R.A.Engh, D.Bossemeyer
Key ref:
M.Gassel et al. (2004). The protein kinase C inhibitor bisindolyl maleimide 2 binds with reversed orientations to different conformations of protein kinase A. J Biol Chem, 279, 23679-23690. PubMed id: 14996846 DOI: 10.1074/jbc.M314082200
Date:
06-Apr-04     Release date:   01-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00517  (KAPCA_BOVIN) -  cAMP-dependent protein kinase catalytic subunit alpha
Seq:
Struc:
351 a.a.
320 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.11  - cAMP-dependent 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     sperm midpiece   11 terms 
  Biological process     regulation of proteasomal protein catabolic process   18 terms 
  Biochemical function     nucleotide binding     13 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M314082200 J Biol Chem 279:23679-23690 (2004)
PubMed id: 14996846  
 
 
The protein kinase C inhibitor bisindolyl maleimide 2 binds with reversed orientations to different conformations of protein kinase A.
M.Gassel, C.B.Breitenlechner, N.König, R.Huber, R.A.Engh, D.Bossemeyer.
 
  ABSTRACT  
 
As the key mediators of eukaryotic signal transduction, the protein kinases often cause disease, and in particular cancer, when disregulated. Appropriately selective protein kinase inhibitors are sought after as research tools and as therapeutic drugs; several have already proven valuable in clinical use. The AGC subfamily protein kinase C (PKC) was identified early as a cause of cancer, leading to the discovery of a variety of PKC inhibitors. Despite its importance and early discovery, no crystal structure for PKC has yet been reported. Therefore, we have co-crystallized PKC inhibitor bisindolyl maleimide 2 (BIM2) with PKA variants to study its binding interactions. BIM2 co-crystallized as an asymmetric pair of kinase-inhibitor complexes. In this asymmetric unit, the two kinase domains have different lobe configurations, and two different inhibitor conformers bind in different orientations. One kinase molecule (A) is partially open with respect to the catalytic conformation, the other (B) represents the most open conformation of PKA reported so far. In monomer A, the BIM2 inhibitor binds tightly via an induced fit in the ATP pocket. The indole moieties are rotated out of the plane with respect to the chemically related but planar inhibitor staurosporine. In molecule B a different conformer of BIM2 binds in a reversed orientation relative to the equivalent maleimide atoms in molecule A. Also, a critical active site salt bridge is disrupted, usually indicating the induction of an inactive conformation. Molecular modeling of the clinical phase III PKC inhibitor LY333531 into the electron density of BIM2 reveals the probable binding mechanism and explains selectivity properties of the inhibitor.
 
  Selected figure(s)  
 
Figure 6.
FIG. 6. Stereo views of the binding pattern of BIM2 in its two orientations in PKA molecules A (intermediate open geometry) and B (wide open geometry). All interacting residues are highlighted). a, molecule A. The hinge region H-bonds Ala^123:N-O32 and Glu121:ON19 are supplemented by an additional Thr183:OG1-O33 H-bond. b, molecule B. Here only the hinge region H-bonds Ala^123:N-O33 and Glu121:O-N19 are formed.
Figure 8.
FIG. 8. Phe^54-inhibitor interaction. a, interaction between Phe^54 and C35 of staurosporine. b, interaction between Phe^54 and C31 of BIM2. The flexibility of Phe^54 and the glycine loop enable it to adapt to different inhibitor configurations and maintain apparently favorable contacts.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 23679-23690) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20336692 M.Rabiller, M.Getlik, S.Klüter, A.Richters, S.Tückmantel, J.R.Simard, and D.Rauh (2010).
Proteus in the world of proteins: conformational changes in protein kinases.
  Arch Pharm (Weinheim), 343, 193-206.  
20336234 O.A.Gani, and R.A.Engh (2010).
Protein kinase inhibition of clinically important staurosporine analogues.
  Nat Prod Rep, 27, 489-498.  
19465915 A.J.Cameron, C.Escribano, A.T.Saurin, B.Kostelecky, and P.J.Parker (2009).
PKC maturation is promoted by nucleotide pocket occupation independently of intrinsic kinase activity.
  Nat Struct Mol Biol, 16, 624-630.  
18978194 E.N.Lavrentyev, and K.U.Malik (2009).
High glucose-induced Nox1-derived superoxides downregulate PKC-betaII, which subsequently decreases ACE2 expression and ANG(1-7) formation in rat VSMCs.
  Am J Physiol Heart Circ Physiol, 296, H106-H118.  
17119643 C.Sánchez, C.Méndez, and J.A.Salas (2006).
Indolocarbazole natural products: occurrence, biosynthesis, and biological activity.
  Nat Prod Rep, 23, 1007-1045.  
17036304 C.S.Page, and P.A.Bates (2006).
Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?
  J Comput Chem, 27, 1990-2007.  
16531242 H.Yamaguchi, M.Kasa, M.Amano, K.Kaibuchi, and T.Hakoshima (2006).
Molecular mechanism for the regulation of rho-kinase by dimerization and its inhibition by fasudil.
  Structure, 14, 589-600.
PDB code: 2f2u
15967991 N.Tapinos, and A.Rambukkana (2005).
Insights into regulation of human Schwann cell proliferation by Erk1/2 via a MEK-independent and p56Lck-dependent pathway from leprosy bacilli.
  Proc Natl Acad Sci U S A, 102, 9188-9193.  
16075446 S.Barrett, S.Bartlett, A.Bolt, A.Ironmonger, C.Joce, A.Nelson, and T.Woodhall (2005).
Configurational stability of bisindolylmaleimide cyclophanes: from conformers to the first configurationally stable, atropisomeric bisindolylmaleimides.
  Chemistry, 11, 6277-6285.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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