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PDBsum entry 2etr

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2etr
Jmol
Contents
Protein chain
400 a.a. *
Ligands
Y27 ×2
Waters ×108
* Residue conservation analysis
PDB id:
2etr
Name: Transferase
Title: Crystal structure of rock i bound to y-27632
Structure: Rho-associated protein kinase 1. Chain: a, b. Fragment: n-terminal and kinase domain, residues 6-415. Synonym: rho-associated, coiled-coil containing protein kinase 1, p160 rock-1, p160rock. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: rock1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.252     R-free:   0.266
Authors: M.Jacobs
Key ref:
M.Jacobs et al. (2006). The structure of dimeric ROCK I reveals the mechanism for ligand selectivity. J Biol Chem, 281, 260-268. PubMed id: 16249185 DOI: 10.1074/jbc.M508847200
Date:
27-Oct-05     Release date:   08-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q13464  (ROCK1_HUMAN) -  Rho-associated protein kinase 1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1354 a.a.
400 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.1  - Non-specific serine/threonine 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!
  Biological process     protein phosphorylation   1 term 
  Biochemical function     transferase activity, transferring phosphorus-containing groups     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M508847200 J Biol Chem 281:260-268 (2006)
PubMed id: 16249185  
 
 
The structure of dimeric ROCK I reveals the mechanism for ligand selectivity.
M.Jacobs, K.Hayakawa, L.Swenson, S.Bellon, M.Fleming, P.Taslimi, J.Doran.
 
  ABSTRACT  
 
ROCK or Rho-associated kinase, a serine/threonine kinase, is an effector of Rho-dependent signaling and is involved in actin-cytoskeleton assembly and cell motility and contraction. The ROCK protein consists of several domains: an N-terminal region, a kinase catalytic domain, a coiled-coil domain containing a RhoA binding site, and a pleckstrin homology domain. The C-terminal region of ROCK binds to and inhibits the kinase catalytic domains, and this inhibition is reversed by binding RhoA, a small GTPase. Here we present the structure of the N-terminal region and the kinase domain. In our structure, two N-terminal regions interact to form a dimerization domain linking two kinase domains together. This spatial arrangement presents the kinase active sites and regulatory sequences on a common face affording the possibility of both kinases simultaneously interacting with a dimeric inhibitory domain or with a dimeric substrate. The kinase domain adopts a catalytically competent conformation; however, no phosphorylation of active site residues is observed in the structure. We also determined the structures of ROCK bound to four different ATP-competitive small molecule inhibitors (Y-27632, fasudil, hydroxyfasudil, and H-1152P). Each of these compounds binds with reduced affinity to cAMP-dependent kinase (PKA), a highly homologous kinase. Subtle differences exist between the ROCK- and PKA-bound conformations of the inhibitors that suggest that interactions with a single amino acid of the active site (Ala215 in ROCK and Thr183 in PKA) determine the relative selectivity of these compounds. Hydroxyfasudil, a metabolite of fasudil, may be selective for ROCK over PKA through a reversed binding orientation.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Overall structure of the ROCK/Y-27632 complex. A, the ROCK protein dimer is drawn with -sheets as arrows and -helices as cylinders. One monomer is drawn in gray, and the others are colored by protein region. The N-terminal dimerization domain is shown in red. The N-terminal kinase domain (dark blue) is shown with the glycine-rich loop drawn in green. The hinge connecting the two domains is colored orange. The C-terminal kinase domain is shown in light blue with the activation loop in purple and the kinase tail in yellow. Y-27632 is shown in the active site near the glycine-rich loop and the hinge. B, a surface representation of the dimer is shown where both monomers are colored by region. Y-27632 is shown in the active site as spheres. A model of the substrate peptide is shown as a pink cylinder and strand, based upon a superposition of the ROCK structure and the PKA/ATP/peptide complex (Protein Data Bank code 1ATP [PDB] ). C and D, an expanded view of the dimerization domain is shown in two orientations, differing by a 90° rotation. All of the structure figures were made with PYMOL (58).
Figure 3.
FIGURE 3. Phosphothreonine-binding site in PKA aligned with ROCK. The activation loops of PKA (gray) and ROCK (green) are shown with interactions between side chains and the phosphate shown as purple dotted lines.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 260-268) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21276421 C.C.Tsai, H.F.Liu, K.C.Hsu, J.M.Yang, C.Chen, K.K.Liu, T.S.Hsu, and J.I.Chao (2011).
7-Chloro-6-piperidin-1-yl-quinoline-5,8-dione (PT-262), a novel ROCK inhibitor blocks cytoskeleton function and cell migration.
  Biochem Pharmacol, 81, 856-865.  
20673774 R.E.Hubbard (2011).
Structure-based drug discovery and protein targets in the CNS.
  Neuropharmacology, 60, 7.  
21394446 X.Zhang, C.Li, H.Gao, H.Nabeka, T.Shimokawa, H.Wakisaka, S.Matsuda, and N.Kobayashi (2011).
Rho kinase inhibitors stimulate the migration of human cultured osteoblastic cells by regulating actomyosin activity.
  Cell Mol Biol Lett, 16, 279-295.  
19942586 D.Huang, T.Zhou, K.Lafleur, C.Nevado, and A.Caflisch (2010).
Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis.
  Bioinformatics, 26, 198-204.  
  20803696 M.Amano, M.Nakayama, and K.Kaibuchi (2010).
Rho-kinase/ROCK: A key regulator of the cytoskeleton and cell polarity.
  Cytoskeleton (Hoboken), 67, 545-554.  
20140017 P.A.Lochhead, G.Wickman, M.Mezna, and M.F.Olson (2010).
Activating ROCK1 somatic mutations in human cancer.
  Oncogene, 29, 2591-2598.  
20854259 P.D.Andrews, M.Becroft, A.Aspegren, J.Gilmour, M.J.James, S.McRae, R.Kime, R.W.Allcock, A.Abraham, Z.Jiang, R.Strehl, J.C.Mountford, G.Milligan, M.D.Houslay, D.R.Adams, and J.A.Frearson (2010).
High-content screening of feeder-free human embryonic stem cells to identify pro-survival small molecules.
  Biochem J, 432, 21-33.  
20516646 S.Chapman, X.Liu, C.Meyers, R.Schlegel, and A.A.McBride (2010).
Human keratinocytes are efficiently immortalized by a Rho kinase inhibitor.
  J Clin Invest, 120, 2619-2626.  
19997641 F.E.Lock, and N.A.Hotchin (2009).
Distinct roles for ROCK1 and ROCK2 in the regulation of keratinocyte differentiation.
  PLoS One, 4, e8190.  
19309729 J.M.Elkins, A.Amos, F.H.Niesen, A.C.Pike, O.Fedorov, and S.Knapp (2009).
Structure of dystrophia myotonica protein kinase.
  Protein Sci, 18, 782-791.
PDB code: 2vd5
19938169 J.Taniguchi, S.Sawai, M.Mori, T.Kubo, K.Kanai, S.Misawa, S.Isose, T.Yamashita, and S.Kuwabara (2009).
Chronic inflammatory demyelinating polyneuropathy sera inhibit axonal growth of mouse dorsal root ganglion neurons by activation of Rho-kinase.
  Ann Neurol, 66, 694-697.  
19296866 L.N.Johnson (2009).
Protein kinase inhibitors: contributions from structure to clinical compounds.
  Q Rev Biophys, 42, 1.  
19740074 R.J.Nichols, N.Dzamko, J.E.Hutti, L.C.Cantley, M.Deak, J.Moran, P.Bamborough, A.D.Reith, and D.R.Alessi (2009).
Substrate specificity and inhibitors of LRRK2, a protein kinase mutated in Parkinson's disease.
  Biochem J, 424, 47-60.  
19718043 V.Hindie, A.Stroba, H.Zhang, L.A.Lopez-Garcia, L.Idrissova, S.Zeuzem, D.Hirschberg, F.Schaeffer, T.J.Jørgensen, M.Engel, P.M.Alzari, and R.M.Biondi (2009).
Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1.
  Nat Chem Biol, 5, 758-764.
PDB codes: 3hrc 3hrf
18946488 D.Komander, R.Garg, P.T.Wan, A.J.Ridley, and D.Barford (2008).
Mechanism of multi-site phosphorylation from a ROCK-I:RhoE complex structure.
  EMBO J, 27, 3175-3185.
PDB code: 2v55
19032760 D.R.Caffrey, E.A.Lunney, and D.J.Moshinsky (2008).
Prediction of specificity-determining residues for small-molecule kinase inhibitors.
  BMC Bioinformatics, 9, 491.  
18973168 H.Schirok, R.Kast, S.Figueroa-Pérez, S.Bennabi, M.J.Gnoth, A.Feurer, H.Heckroth, M.Thutewohl, H.Paulsen, A.Knorr, J.Hütter, M.Lobell, K.Münter, V.Geiss, H.Ehmke, D.Lang, M.Radtke, J.Mittendorf, and J.P.Stasch (2008).
Design and synthesis of potent and selective azaindole-based Rho kinase (ROCK) inhibitors.
  ChemMedChem, 3, 1893-1904.  
18634988 P.Holvoet, and P.Sinnaeve (2008).
Angio-associated migratory cell protein and smooth muscle cell migration in development of restenosis and atherosclerosis.
  J Am Coll Cardiol, 52, 312-314.  
  18827856 T.Kubo, A.Yamaguchi, N.Iwata, and T.Yamashita (2008).
The therapeutic effects of Rho-ROCK inhibitors on CNS disorders.
  Ther Clin Risk Manag, 4, 605-615.  
17934515 R.Kast, H.Schirok, S.Figueroa-Pérez, J.Mittendorf, M.J.Gnoth, H.Apeler, J.Lenz, J.K.Franz, A.Knorr, J.Hütter, M.Lobell, K.Zimmermann, K.Münter, K.H.Augstein, H.Ehmke, and J.P.Stasch (2007).
Cardiovascular effects of a novel potent and highly selective azaindole-based inhibitor of Rho-kinase.
  Br J Pharmacol, 152, 1070-1080.  
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.  
17084073 M.G.Gold, D.Barford, and D.Komander (2006).
Lining the pockets of kinases and phosphatases.
  Curr Opin Struct Biol, 16, 693-701.  
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.