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PDBsum entry 1b39

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protein ligands metals links
Transferase PDB id
1b39
Jmol
Contents
Protein chain
291 a.a. *
Ligands
ATP
Metals
_MG
Waters ×145
* Residue conservation analysis
PDB id:
1b39
Name: Transferase
Title: Human cyclin-dependent kinase 2 phosphorylated on thr 160
Structure: Protein (cell division protein kinase 2). Chain: a. Fragment: intact. Synonym: p33 protein kinase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9.
Resolution:
2.10Å     R-factor:   0.200     R-free:   0.270
Authors: N.R.Brown,M.E.M.Noble,A.M.Lawrie,M.C.Morris,P.Tunnah, G.Divita,L.N.Johnson,J.A.Endicott
Key ref:
N.R.Brown et al. (1999). Effects of phosphorylation of threonine 160 on cyclin-dependent kinase 2 structure and activity. J Biol Chem, 274, 8746-8756. PubMed id: 10085115 DOI: 10.1074/jbc.274.13.8746
Date:
17-Dec-98     Release date:   23-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2
Seq:
Struc:
298 a.a.
290 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.22  - Cyclin-dependent 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     cyclin-dependent protein kinase holoenzyme complex   15 terms 
  Biological process     regulation of gene silencing   27 terms 
  Biochemical function     nucleotide binding     12 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.274.13.8746 J Biol Chem 274:8746-8756 (1999)
PubMed id: 10085115  
 
 
Effects of phosphorylation of threonine 160 on cyclin-dependent kinase 2 structure and activity.
N.R.Brown, M.E.Noble, A.M.Lawrie, M.C.Morris, P.Tunnah, G.Divita, L.N.Johnson, J.A.Endicott.
 
  ABSTRACT  
 
We have prepared phosphorylated cyclin-dependent protein kinase 2 (CDK2) for crystallization using the CDK-activating kinase 1 (CAK1) from Saccharomyces cerevisiae and have grown crystals using microseeding techniques. Phosphorylation of monomeric human CDK2 by CAK1 is more efficient than phosphorylation of the binary CDK2-cyclin A complex. Phosphorylated CDK2 exhibits histone H1 kinase activity corresponding to approximately 0.3% of that observed with the fully activated phosphorylated CDK2-cyclin A complex. Fluorescence measurements have shown that Thr160 phosphorylation increases the affinity of CDK2 for both histone substrate and ATP and decreases its affinity for ADP. By contrast, phosphorylation of CDK2 has a negligible effect on the affinity for cyclin A. The crystal structures of the ATP-bound forms of phosphorylated CDK2 and unphosphorylated CDK2 have been solved at 2.1-A resolution. The structures are similar, with the major difference occurring in the activation segment, which is disordered in phosphorylated CDK2. The greater mobility of the activation segment in phosphorylated CDK2 and the absence of spontaneous crystallization suggest that phosphorylated CDK2 may adopt several different mobile states. The majority of these states are likely to correspond to inactive conformations, but a small fraction of phosphorylated CDK2 may be in an active conformation and hence explain the basal activity observed.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. CDK-associated phosphatase KAP dephosphorylates phosphorylated CDK2. KAP specifically dephosphorylates monomeric phosphorylated CDK2.
Figure 6.
Fig. 6. a, the fold of monomeric CDK2. The structure is shown in a schematic representation with regions of -sheet shown as arrows and -helix shown as ribbons. The N-terminal domain is colored principally white, with the exception of the glycine-rich loop (colored magenta), and the C-helix (PSTAIRE helix, colored gold). The region of the N-terminal domain for which no trace is visible (residues 36-43) is indicated by small black spheres identifying residues 35 and 44. ATP is shown in ball and stick representation at the interface between the N- and C-terminal domains. The C-terminal domain is colored pink, with the activation segment (residues 145-172) highlighted in cyan. b, comparison of electron density for the tip of the activation segment. The upper stereo pair shows electron density defining the conformation of residues at the tip of the activation segment (residues 155-165) in the ATP complex of unphosphorylated monomeric CDK2, while the lower stereo pair shows the equivalent electron density in phosphorylated monomeric CDK2. In this figure the phosphate group attached to Thr^160 has been omitted from the phosphorylated CDK2 structure for clarity. The maps were calculated using (2F[o] F[c]) [calc] coefficients generated by REFMAC and are contoured at a level of 0.2e^ Å^ 3. c, B-factor plots for CDK2-ATP and phosphorylated CDK2-ATP. The mean main chain B-factor of each residue along the polypeptide chain is shown for unphosphorylated CDK2 (thin lines) and phosphorylated CDK2 (thick lines). The outstanding regions of difference include the glycine loop (residues 8-18) and the tip of the activation segment (residues 155-165). d, detail of the fold of the CDK2-ATP complex. The interaction of Tyr^159 and Thr^160, at the tip of the activation segment, with residues Glu^12-Tyr^15 in the glycine-rich loop is shown. The coloring scheme is the same as for a.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 8746-8756) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
20971646 S.S.Taylor, and A.P.Kornev (2011).
Protein kinases: evolution of dynamic regulatory proteins.
  Trends Biochem Sci, 36, 65-77.  
20338198 F.C.Gomes, N.O.Ali, E.Brown, R.G.Walker, K.M.Grant, and J.C.Mottram (2010).
Recombinant Leishmania mexicana CRK3:CYCA has protein kinase activity in the absence of phosphorylation on the T-loop residue Thr178.
  Mol Biochem Parasitol, 171, 89-96.  
20397180 L.Kurzawa, and M.C.Morris (2010).
Cell-cycle markers and biosensors.
  Chembiochem, 11, 1037-1047.  
20162627 O.Doppelt-Azeroual, F.Delfaud, F.Moriaud, and A.G.de Brevern (2010).
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.
  Protein Sci, 19, 847-867.  
21134645 T.N.Lombana, N.Echols, M.C.Good, N.D.Thomsen, H.L.Ng, A.E.Greenstein, A.M.Falick, D.S.King, and T.Alber (2010).
Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB.
  Structure, 18, 1667-1677.
PDB code: 3orm
19237555 T.Takaki, A.Echalier, N.R.Brown, T.Hunt, J.A.Endicott, and M.E.Noble (2009).
The structure of CDK4/cyclin D3 has implications for models of CDK activation.
  Proc Natl Acad Sci U S A, 106, 4171-4176.
PDB code: 3g33
18239682 A.C.Pike, P.Rellos, F.H.Niesen, A.Turnbull, A.W.Oliver, S.A.Parker, B.E.Turk, L.H.Pearl, and S.Knapp (2008).
Activation segment dimerization: a mechanism for kinase autophosphorylation of non-consensus sites.
  EMBO J, 27, 704-714.
PDB codes: 2j51 2j7t 2j90 2jfl 2jfm 2uv2
18443039 A.K.Mandal, N.B.Nillegoda, J.A.Chen, and A.J.Caplan (2008).
Ydj1 protects nascent protein kinases from degradation and controls the rate of their maturation.
  Mol Cell Biol, 28, 4434-4444.  
18041759 B.Seebeck, I.Reulecke, A.Kämper, and M.Rarey (2008).
Modeling of metal interaction geometries for protein-ligand docking.
  Proteins, 71, 1237-1254.  
18042686 I.Bártová, J.Koca, and M.Otyepka (2008).
Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation.
  Protein Sci, 17, 22-33.  
18470542 I.Bártová, J.Koca, and M.Otyepka (2008).
Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations.
  J Mol Model, 14, 761-768.  
18184589 J.Eswaran, A.Bernad, J.M.Ligos, B.Guinea, J.E.Debreczeni, F.Sobott, S.A.Parker, R.Najmanovich, B.E.Turk, and S.Knapp (2008).
Structure of the human protein kinase MPSK1 reveals an atypical activation loop architecture.
  Structure, 16, 115-124.  
18703838 R.A.Elling, R.V.Fucini, and M.J.Romanowski (2008).
Structures of the wild-type and activated catalytic domains of Brachydanio rerio Polo-like kinase 1 (Plk1): changes in the active-site conformation and interactions with ligands.
  Acta Crystallogr D Biol Crystallogr, 64, 909-918.
PDB codes: 3d5u 3d5v 3d5w 3d5x
17709340 J.L.Chung, J.E.Beaver, E.D.Scheeff, and P.E.Bourne (2007).
Con-Struct Map: a comparative contact map analysis tool.
  Bioinformatics, 23, 2491-2492.  
17541419 M.P.Mazanetz, and P.M.Fischer (2007).
Untangling tau hyperphosphorylation in drug design for neurodegenerative diseases.
  Nat Rev Drug Discov, 6, 464-479.  
16628247 E.S.Groban, A.Narayanan, and M.P.Jacobson (2006).
Conformational changes in protein loops and helices induced by post-translational phosphorylation.
  PLoS Comput Biol, 2, e32.  
16584130 J.Sridhar, N.Akula, and N.Pattabiraman (2006).
Selectivity and potency of cyclin-dependent kinase inhibitors.
  AAPS J, 8, E204-E221.  
16292742 M.De Vivo, A.Cavalli, G.Bottegoni, P.Carloni, and M.Recanatini (2006).
Role of phosphorylated Thr160 for the activation of the CDK2/Cyclin A complex.
  Proteins, 62, 89-98.  
16191191 A.Cheng, S.Gerry, P.Kaldis, and M.J.Solomon (2005).
Biochemical characterization of Cdk2-Speedy/Ringo A2.
  BMC Biochem, 6, 19.  
15660127 R.Honda, E.D.Lowe, E.Dubinina, V.Skamnaki, A.Cook, N.R.Brown, and L.N.Johnson (2005).
The structure of cyclin E1/CDK2: implications for CDK2 activation and CDK2-independent roles.
  EMBO J, 24, 452-463.
PDB code: 1w98
15988018 Z.Fu, M.J.Schroeder, J.Shabanowitz, P.Kaldis, K.Togawa, A.K.Rustgi, D.F.Hunt, and T.W.Sturgill (2005).
Activation of a nuclear Cdc2-related kinase within a mitogen-activated protein kinase-like TDY motif by autophosphorylation and cyclin-dependent protein kinase-activating kinase.
  Mol Cell Biol, 25, 6047-6064.  
15147518 M.D.Niculescu, Y.Yamamuro, and S.H.Zeisel (2004).
Choline availability modulates human neuroblastoma cell proliferation and alters the methylation of the promoter region of the cyclin-dependent kinase inhibitor 3 gene.
  J Neurochem, 89, 1252-1259.  
14988503 M.Hallberg, G.V.Polozkov, G.Z.Hu, J.Beve, C.M.Gustafsson, H.Ronne, and S.Björklund (2004).
Site-specific Srb10-dependent phosphorylation of the yeast Mediator subunit Med2 regulates gene expression from the 2-microm plasmid.
  Proc Natl Acad Sci U S A, 101, 3370-3375.  
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
15341724 N.LaRonde-LeBlanc, and A.Wlodawer (2004).
Crystal structure of A. fulgidus Rio2 defines a new family of serine protein kinases.
  Structure, 12, 1585-1594.
PDB codes: 1tqi 1tqm 1tqp
14580330 D.M.Glover (2003).
Aurora A on the mitotic spindle is activated by the way it holds its partner.
  Mol Cell, 12, 797-799.  
12897769 M.A.Seeliger, S.E.Breward, A.Friedler, O.Schon, and L.S.Itzhaki (2003).
Cooperative organization in a macromolecular complex.
  Nat Struct Biol, 10, 718-724.  
12556199 N.C.Waters, and J.A.Geyer (2003).
Cyclin-dependent protein kinases as therapeutic drug targets for antimalarial drug development.
  Expert Opin Ther Targets, 7, 7.  
14580337 R.Bayliss, T.Sardon, I.Vernos, and E.Conti (2003).
Structural basis of Aurora-A activation by TPX2 at the mitotic spindle.
  Mol Cell, 12, 851-862.
PDB codes: 1ol5 1ol6 1ol7
  11781350 J.L.Donato, J.Ko, J.L.Kutok, T.Cheng, T.Shirakawa, X.Q.Mao, D.Beach, D.T.Scadden, M.H.Sayegh, and C.N.Adra (2002).
Human HTm4 is a hematopoietic cell cycle regulator.
  J Clin Invest, 109, 51-58.  
11891112 K.E.Prehoda, and W.A.Lim (2002).
How signaling proteins integrate multiple inputs: a comparison of N-WASP and Cdk2.
  Curr Opin Cell Biol, 14, 149-154.  
12081504 L.M.Stevenson, M.S.Deal, J.C.Hagopian, and J.Lew (2002).
Activation mechanism of CDK2: role of cyclin binding versus phosphorylation.
  Biochemistry, 41, 8528-8534.  
12191604 L.N.Johnson, E.De Moliner, N.R.Brown, H.Song, D.Barford, J.A.Endicott, and M.E.Noble (2002).
Structural studies with inhibitors of the cell cycle regulatory kinase cyclin-dependent protein kinase 2.
  Pharmacol Ther, 93, 113-124.  
12191603 R.A.Engh, and D.Bossemeyer (2002).
Structural aspects of protein kinase control-role of conformational flexibility.
  Pharmacol Ther, 93, 99.  
11746695 A.Cavalli, C.Dezi, G.Folkers, L.Scapozza, and M.Recanatini (2001).
Three-dimensional model of the cyclin-dependent kinase 1 (CDK1): Ab initio active site parameters for molecular dynamics studies of CDKS.
  Proteins, 45, 478-485.  
11506705 C.Ellenrieder, B.Bartosch, G.Y.Lee, M.Murphy, C.Sweeney, M.Hergersberg, M.Carrington, R.Jaussi, and T.Hunt (2001).
The long form of CDK2 arises via alternative splicing and forms an active protein kinase with cyclins A and E.
  DNA Cell Biol, 20, 413-423.  
11463386 H.Song, N.Hanlon, N.R.Brown, M.E.Noble, L.N.Johnson, and D.Barford (2001).
Phosphoprotein-protein interactions revealed by the crystal structure of kinase-associated phosphatase in complex with phosphoCDK2.
  Mol Cell, 7, 615-626.
PDB codes: 1fpz 1fq1
11532001 J.K.Holmes, and M.J.Solomon (2001).
The role of Thr160 phosphorylation of Cdk2 in substrate recognition.
  Eur J Biochem, 268, 4647-4652.  
11732181 P.C.John, M.Mews, and R.Moore (2001).
Cyclin/Cdk complexes: their involvement in cell cycle progression and mitotic division.
  Protoplasma, 216, 119-142.  
  11739795 P.Kaldis, P.M.Ojala, L.Tong, T.P.Mäkelä, and M.J.Solomon (2001).
CAK-independent activation of CDK6 by a viral cyclin.
  Mol Biol Cell, 12, 3987-3999.  
  10747052 F.R.Cross, and K.Levine (2000).
Genetic analysis of the relationship between activation loop phosphorylation and cyclin binding in the activation of the Saccharomyces cerevisiae Cdc28p cyclin-dependent kinase.
  Genetics, 154, 1549-1559.  
11114073 R.L.Rich, and D.G.Myszka (2000).
Skerra A, 2000. Engineered scaffolds for molecular recognition. Journal of Molecular Recognition13:167-187.
  J Mol Recognit, 13, 409-410.  
10966577 X.Zhou, F.Alber, G.Folkers, G.H.Gonnet, and G.Chelvanayagam (2000).
An analysis of the helix-to-strand transition between peptides with identical sequence.
  Proteins, 41, 248-256.  
10607671 J.A.Endicott, M.E.Noble, and J.A.Tucker (1999).
Cyclin-dependent kinases: inhibition and substrate recognition.
  Curr Opin Struct Biol, 9, 738-744.  
10518216 K.Levine, L.Kiang, M.D.Jacobson, R.P.Fisher, and F.R.Cross (1999).
Directed evolution to bypass cyclin requirements for the Cdc28p cyclin-dependent kinase.
  Mol Cell, 4, 353-363.  
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.