Primary Citation PubMed: 8756328
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Conformational changes in protein loops and helices induced by post-translational phosphorylation.
(2006) PLoS Comput Biol 2
PubMed: 16628247 | PubMedCentral: PMC1440919 | DOI: 10.1371/journal.pcbi.0020032
Accession Numbers The Protein Data Bank ( http://www.rcsb.org/pdb ) accession numbers for the proteins discussed in this paper are as follows: β PGM, (PDB ID: 1LVH); CDK2, phosphorylated (PDB ... D: 1JST); CDK2, unphosphorylated (PDB ID: 1FIN); CDK2/KAP complex (PDB ID: 1FQ1); cyclin A (PDB ID: 1B39); ERK2, phosphorylated (PDB ID: 2ERK); ERK2, unphosphorylated (PDB ID: 1ERK); FixJ, phosphorylated (PDB ID: 1D5W); FixJ, unphosphorylated (PDB ID: 1DCK); GLM, (PDB ID: 1MKI); Hpr, phosphorylated (PDB ID: 1FU0); Hpr, unphosphorylated (PDB ID: 1PTF); LCK, (PDB ID: 3LCK); Pim1, (PDB ID: 2BIK); PMM, (PDB ID: 1K35); Psp, phosphorylated (PDB ID: 1J97); Psp, unphosphorylated (PDB ID: 1L7O); P38 γ, (PDB ID: 1CM8); SpoIIAA, phosphorylated (PDB ID: 1H4X); and SpoIIAA, unphosphorylated (PDB ID: 1H4Z); Spo0A, (PDB ID: 1QMP).
Publication Year: 2006
Conservation, variability and the modeling of active protein kinases.
(2007) PLoS One 2
PubMed: 17912359 | PubMedCentral: PMC1989141 | DOI: 10.1371/journal.pone.0000982
* Kinase Full name Species PDB code Pfam domain (residues) ACK1 activated CDC42 kinase 1 H. sapiens 1U54  Protein tyrosine kinase (126-385) Akt2 RAC-β serine/threon... ne-protein kinase H. sapiens 1O6K  Protein kinase (152-409) CDK2 cell division protein kinase 2 H. sapiens 1JST  Protein kinase (4-286) CK1 casein kinase I S. pombe 1CSN  Protein kinase (12-237) CK2 casein kinase II subunit α Z. mays 1LP4  Protein kinase (34-319) DAPK death-associated protein kinase H. sapiens 1IG1  Protein kinase (13-275) IRK insulin receptor tyrosine kinase H. sapiens 1IR3  Protein tyrosine kinase (1023-1290) MAPK p38γ mitogen-activated protein kinase p38γ H. sapiens 1CM8  Protein kinase (27-311) PhK phosphorylase kinase O. cuniculus 1PHK  Protein kinase (19-287) Pim-1 proto-oncogene serine/threonine-protein kinase Pim-1 H. sapiens 1XR1  Protein kinase (129-381) PKA protein kinase A M. musculus 1ATP  Protein kinase (43-297) PknB probable serine/threonine-protein kinase PknB M. tuberculosis 1MRU  Protein kinase (11-273) Rio2 Rio2 serine kinase A. fulgidus 1ZAO  Rio1 family (105-275) Sky1P SR protein kinase S. cerevisiae 1Q97  Protein kinase (158-706) † TAO2 thousand and one amino-acid protein 2 R. norvegicus 1U5R  Protein kinase (28-281) ChaK ‡ transient receptor potential channel kinase M. musculus 1IA9  Alpha kinase (1596-1814) * The average pair-wise sequence identity between this set as computed by ClustalW using its default parameters is 17%.
Publication Year: 2007
ATP and MO25alpha regulate the conformational state of the STRADalpha pseudokinase and activation of the LKB1 tumour suppressor.
(2009) PLoS Biol 7
PubMed: 19513107 | PubMedCentral: PMC2686265 | DOI: 10.1371/journal.pbio.1000126
Residues from the C-lobe of STRADα (152–431) were superimposed onto the structures of inactive CDK2 (PDB ID 1HCK  ) and EGFR kinase (PDB ID 2GS7), and active CDK2 (... DB ID 1JST) and EGFR (PDB ID 2GS2).
Publication Year: 2009
Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates.
(2010) Nat Struct Mol Biol 17
PubMed: 19966800 | PubMedCentral: PMC3006182 | DOI: 10.1038/nsmb.1705
Cdk2 (PDB ID 1JST) and PKA (PDB ID 1ATP) are from structures of the kinases in activated states (including Cdk2 bound to cyclinA with activating phosphorylation of threonine).
Publication Year: 2010
A cancer-derived mutation in the PSTAIRE helix of cyclin-dependent kinase 2 alters the stability of cyclin binding.
(2010) Biochim Biophys Acta 1803
PubMed: 20399812 | PubMedCentral: PMC3111755 | DOI: 10.1016/j.bbamcr.2010.04.004
The cdk2 starting structure (PDB code: 2CLX, resolution 1.8 Å with the ligand removed from the active site  ) and the starting structure for pT160-cdk2/ATP complexed with Cyclin E ... as taken from PDB (PDB code: 1W98, resolution 2.15 Å  , where ATP and Mg 2+ was added from 1JST structure  ).
Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21.
(2011) Nat Chem Biol 7
PubMed: 21358637 | PubMedCentral: PMC3124363 | DOI: 10.1038/nchembio.536
Sub-domain LH of p21 ( a ) and the other Cip/Kip proteins can stretch to accommodate the varied orientations of the Cdk and cyclin subunits of Cdk/cyclin complexes that regulate cell division, includi... g ( b ) Cdk2/cyclin A and ( c ) Cdk4/cyclin D3, for which high-resolution structural data is available (PDB files 1JST 17 and 3G33 39 , respectively), as well as ( d ) other, uncharacterized Cdk/cyclin complexes that regulate cell division.
Cdk/cyclin complex Distance (Å) 1 PDB ID Cdk2/cyclin A 36.2 1JST 17 Cdk2/cyclin B1 36.5 2JGZ 36 Cdk2/cyclin E1 35.8 1W98 37 Cdk4/cyclin D1 34.0 2W96 38 Cdk4/cyclin D3 34.0 3G33 39 1 Distances were measured between the C α atoms of a conserved Val residue in the Cdks (Val 30 in Cdk2 and Val 32 in Cdk4) and a conserved Leu residue in the cyclins [Leu 255 in cyclin A, Leu 190 (isoform 1) in cyclin E1, Leu 246 in cyclin B, and Leu 101 in cyclins D1 and D3].
Publication Year: 2011
Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase.
(2012) J Am Chem Soc 134
PubMed: 22891849 | PubMedCentral: PMC3446636 | DOI: 10.1021/ja304419t
The backbone rmsd from ADP·2Mg structure to 1JST (a complex with ATPγS·Mn 2+ ) = 1.24 Å, 1QMZ (AMPPNP·Mg 2+ /peptide) = 0.65 Å, 3QHR (ADP·2Mg/Mg... 3 – /peptide TS) = 0.57 Å.
(C) Two Mg 2+ ions are identified in the ADP·2Mg structure (maroon) but not ATPγS-bound pCDK2 (gray, 1JST) 3 or AMPPNP-bound pCDK2 (black, 1QMZ).
Publication Year: 2012
On the molecular mechanisms of mitotic kinase activation.
(2012) Open Biol 2
PubMed: 23226601 | PubMedCentral: PMC3513839 | DOI: 10.1098/rsob.120136
( d ) The phosphorylated Cdk2/Cyclin A structure (PDB code 1JST) resembles that of active PKA, with all the expected interactions in place.
(ii) The active conformation of Cdk2-Cyclin A (PDB code 1JST), with the cyclin shown as a green surface.
A structure-guided approach for protein pocket modeling and affinity prediction.
(2013) J Comput Aided Mol Des 27
PubMed: 24214361 | PubMedCentral: PMC3851759 | DOI: 10.1007/s10822-013-9688-9
PDB codes of the pool of protein structures considered for model guidance in the CDK2 study: 1AQ1, 1FVT, 1FVV, 1GIH, 1B38, 1B39, 1FIN, 1FQ1, 1GY3, 1HCK, 1JST, 1QMZ, 1H08, 1DI8, 1H01, 1H00, 1E9H, 1JVP,... 1KE5, 1KE6, 1KE7, 1KE8, 1KE9, 1H07, 1E1X, 1JSV 26.
Publication Year: 2013
PubMed ID is not available.
Published in 2014
Upon binding of cyclin A (right: [PDB: 1JST]), the C-helix and the activation domain are pulled apart - a configuration that is further fixed by phosphorylation of residue T160, making the catalytic p... cket accessible for enzymatic activity.
Publication Year: 2014
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