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PDBsum entry 1q24

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protein ligands metals Protein-protein interface(s) links
Transferase/transferase inhibitor PDB id
1q24
Jmol
Contents
Protein chains
337 a.a. *
20 a.a. *
Ligands
ATP
Metals
_MG
Waters ×132
* Residue conservation analysis
PDB id:
1q24
Name: Transferase/transferase inhibitor
Title: Pka double mutant model of pkb in complex with mgatp
Structure: Camp-dependent protein kinase, alpha-catalytic subunit. Chain: a. Synonym: pka c-alpha. Engineered: yes. Mutation: yes. Camp-dependent protein kinase inhibitor, alpha form. Chain: i.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Gene: prkaca. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: the protein was chemically synthesized. The sequence of the protein is naturally found in homo sapiens.
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.202     R-free:   0.250
Authors: M.Gassel,C.B.Breitenlechner,P.Rueger,U.Jucknischke, T.Schneider,R.Huber,D.Bossemeyer,R.A.Engh
Key ref:
M.Gassel et al. (2003). Mutants of protein kinase A that mimic the ATP-binding site of protein kinase B (AKT). J Mol Biol, 329, 1021-1034. PubMed id: 12798691 DOI: 10.1016/S0022-2836(03)00518-7
Date:
23-Jul-03     Release date:   19-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00517  (KAPCA_BOVIN) -  cAMP-dependent protein kinase catalytic subunit alpha
Seq:
Struc:
351 a.a.
337 a.a.*
Protein chain
Pfam   ArchSchema ?
Q71U53  (IPKA_PIG) -  cAMP-dependent protein kinase inhibitor alpha
Seq:
Struc:
76 a.a.
20 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.2.7.11.11  - cAMP-dependent protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+ 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: 10.1016/S0022-2836(03)00518-7 J Mol Biol 329:1021-1034 (2003)
PubMed id: 12798691  
 
 
Mutants of protein kinase A that mimic the ATP-binding site of protein kinase B (AKT).
M.Gassel, C.B.Breitenlechner, P.Rüger, U.Jucknischke, T.Schneider, R.Huber, D.Bossemeyer, R.A.Engh.
 
  ABSTRACT  
 
The mutation of well behaved enzymes in order to simulate less manageable cognates is the obvious approach to study specific features of the recalcitrant target. Accordingly, the prototypical protein kinase PKA serves as a model for many kinases, including the closely related PKB, an AGC family protein kinase now implicated as oncogenic in several cancers. Two residues that differ between the alpha isoforms of PKA and PKB at the adenine-binding site generate differing shapes of the binding surface and are likely to play a role in ligand selectivity. As the corresponding mutations in PKA, V123A would enlarge the adenine pocket, while L173M would alter both the shape and its electronic character of the adenine-binding surface. We have determined the structures of the corresponding double mutant (PKAB2: PKAalpha V123A, L173M) in apo and MgATP-bound states, and observed structural alterations of a residue not previously involved in ATP-binding interactions: the side-chain of Q181, which in native PKA points away from the ATP-binding site, adopts in apo double mutant protein a new rotamer conformation, which places the polar groups at the hinge region in the ATP pocket. MgATP binding forces Q181 back to the position seen in native PKA. The crystal structure shows that ATP binding geometry is identical with that in native PKA but in this case was determined under conditions with only a single Mg ion ligand. Surface plasmon resonance spectroscopy studies show that significant energy is required for this ligand-induced transition. An additional PKA/PKB mutation, Q181K, corrects the defect, as shown both by the crystal structure of triple mutant PKAB3 (PKAalpha V123A, L173M, Q181K) and by surface plasmon resonance spectroscopy binding studies with ATP and three isoquinoline inhibitors. Thus, the triple mutant serves well as an easily crystallizable model for PKB inhibitor interactions. Further, the phenomenon of Q181 shows how crystallographic analysis should accompany mutant studies to monitor possible spurious structural effects.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Sim-weighted electron density (2mF[o] -dF[c], blue at 1s) and difference electron density (mF[o] -dF[c], white at 2s and red at -2s) maps showing the rotation of Q181. The maps were calculated from a model of PKA (orange sticks) after refinement but prior to rotation of the side-chain. Green sticks depict the refined structure of the double mutant PKAB2. The density shows unambiguously how Q181 rotates to occupy the cavity near the V123A position and near the adenine-binding interaction sites.
Figure 5.
Figure 5. Stereo view of an overlay of the MgATP-PKAB2 complex structure (multicolored by atom type) and the MnAMP-PNP-PKA complex structure (green sticks, PDB code 1CDK[16.]). The 2F[o] -F[c] density (1s) belongs to PKAB2 liganded with ATP. The PKAB2 structure is the first Mg ATP-PKA structure and shows only a single bound metal ion.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 329, 1021-1034) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19918057 J.Eswaran, D.Patnaik, P.Filippakopoulos, F.Wang, R.L.Stein, J.W.Murray, J.M.Higgins, and S.Knapp (2009).
Structure and functional characterization of the atypical human kinase haspin.
  Proc Natl Acad Sci U S A, 106, 20198-20203.
PDB codes: 2vuw 3dlz 3iq7
19043747 M.Muddassar, F.A.Pasha, M.M.Neaz, Y.Saleem, and S.J.Cho (2009).
Elucidation of binding mode and three dimensional quantitative structure-activity relationship studies of a novel series of protein kinase B/Akt inhibitors.
  J Mol Model, 15, 183-192.  
19339067 R.L.van Montfort, and P.Workman (2009).
Structure-based design of molecular cancer therapeutics.
  Trends Biotechnol, 27, 315-328.  
18794885 C.Garcia-Echeverria, and W.R.Sellers (2008).
Drug discovery approaches targeting the PI3K/Akt pathway in cancer.
  Oncogene, 27, 5511-5526.  
16249095 I.Collins, J.Caldwell, T.Fonseca, A.Donald, V.Bavetsias, L.J.Hunter, M.D.Garrett, M.G.Rowlands, G.W.Aherne, T.G.Davies, V.Berdini, S.J.Woodhead, D.Davis, L.C.Seavers, P.G.Wyatt, P.Workman, and E.McDonald (2006).
Structure-based design of isoquinoline-5-sulfonamide inhibitors of protein kinase B.
  Bioorg Med Chem, 14, 1255-1273.
PDB codes: 2c1a 2c1b
16699172 S.Bonn, S.Herrero, C.B.Breitenlechner, A.Erlbruch, W.Lehmann, R.A.Engh, M.Gassel, and D.Bossemeyer (2006).
Structural analysis of protein kinase A mutants with Rho-kinase inhibitor specificity.
  J Biol Chem, 281, 24818-24830.
PDB codes: 2gfc 2gnf 2gng 2gnh 2gni 2gnj 2gnl
15549676 R.L.Rich, and D.G.Myszka (2005).
Survey of the year 2003 commercial optical biosensor literature.
  J Mol Recognit, 18, 1.  
14996846 M.Gassel, C.B.Breitenlechner, N.König, R.Huber, R.A.Engh, and D.Bossemeyer (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.
PDB code: 1szm
15481030 T.Langer, M.Vogtherr, B.Elshorst, M.Betz, U.Schieborr, K.Saxena, and H.Schwalbe (2004).
NMR backbone assignment of a protein kinase catalytic domain by a combination of several approaches: application to the catalytic subunit of cAMP-dependent protein kinase.
  Chembiochem, 5, 1508-1516.  
15364937 Z.B.Xu, D.Chaudhary, S.Olland, S.Wolfrom, R.Czerwinski, K.Malakian, L.Lin, M.L.Stahl, D.Joseph-McCarthy, C.Benander, L.Fitz, R.Greco, W.S.Somers, and L.Mosyak (2004).
Catalytic domain crystal structure of protein kinase C-theta (PKCtheta).
  J Biol Chem, 279, 50401-50409.
PDB code: 1xjd
14656443 C.Breitenlechner, M.Gassel, H.Hidaka, V.Kinzel, R.Huber, R.A.Engh, and D.Bossemeyer (2003).
Protein kinase A in complex with Rho-kinase inhibitors Y-27632, Fasudil, and H-1152P: structural basis of selectivity.
  Structure, 11, 1595-1607.
PDB codes: 1q8t 1q8u 1q8w
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 codes are shown on the right.