2cch

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[[Image:2cch.gif|left|200px]]<br /><applet load="2cch" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2cch, resolution 1.70&Aring;" />
 
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'''THE CRYSTAL STRUCTURE OF CDK2 CYCLIN A IN COMPLEX WITH A SUBSTRATE PEPTIDE DERIVED FROM CDC MODIFIED WITH A GAMMA-LINKED ATP ANALOGUE'''<br />
 
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==Overview==
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==The crystal structure of CDK2 cyclin A in complex with a substrate peptide derived from CDC modified with a gamma-linked ATP analogue==
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Phospho-CDK2/cyclin A, a kinase that is active in cell cycle S phase, contains an RXL substrate recognition site that is over 40 A from the, catalytic site. The role of this recruitment site, which enhances, substrate affinity and catalytic efficiency, has been investigated using, peptides derived from the natural substrates, namely CDC6 and p107, and a, bispeptide inhibitor in which the gamma-phosphate of ATP is covalently, attached by a linker to the CDC6 substrate peptide. X-ray studies with a, 30-residue CDC6 peptide in complex with pCDK2/cyclin A showed binding of a, dodecamer peptide at the recruitment site and a heptapeptide at the, catalytic site, but no density for the linking 11 residues. Kinetic, studies established that the CDC6 peptide had an 18-fold lower Km compared, with heptapeptide substrate and that this effect required the recruitment, peptide to be covalently linked to the substrate peptide. X-ray studies, with the CDC6 bispeptide showed binding of the dodecamer at the, recruitment site and the modified ATP in two alternative conformations at, the catalytic site. The CDC6 bispeptide was a potent inhibitor competitive, with both ATP and peptide substrate of pCDK2/cyclin A activity against a, heptapeptide substrate (Ki = 0.83 nm) but less effective against, RXL-containing substrates. We discuss how localization at the recruitment, site (KD 0.4 microm) leads to increased catalytic efficiency and the, design of a potent inhibitor. The notion of a flexible linker between the, sites, which must have more than a minimal number of residues, provides an, explanation for recognition and discrimination against different, substrates.
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<StructureSection load='2cch' size='340' side='right'caption='[[2cch]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2cch]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CCH FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cch FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cch OCA], [https://pdbe.org/2cch PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cch RCSB], [https://www.ebi.ac.uk/pdbsum/2cch PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cch ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CDK2_HUMAN CDK2_HUMAN] Serine/threonine-protein kinase involved in the control of the cell cycle; essential for meiosis, but dispensable for mitosis. Phosphorylates CTNNB1, USP37, p53/TP53, NPM1, CDK7, RB1, BRCA2, MYC, NPAT, EZH2. Interacts with cyclins A, B1, B3, D, or E. Triggers duplication of centrosomes and DNA. Acts at the G1-S transition to promote the E2F transcriptional program and the initiation of DNA synthesis, and modulates G2 progression; controls the timing of entry into mitosis/meiosis by controlling the subsequent activation of cyclin B/CDK1 by phosphorylation, and coordinates the activation of cyclin B/CDK1 at the centrosome and in the nucleus. Crucial role in orchestrating a fine balance between cellular proliferation, cell death, and DNA repair in human embryonic stem cells (hESCs). Activity of CDK2 is maximal during S phase and G2; activated by interaction with cyclin E during the early stages of DNA synthesis to permit G1-S transition, and subsequently activated by cyclin A2 (cyclin A1 in germ cells) during the late stages of DNA replication to drive the transition from S phase to mitosis, the G2 phase. EZH2 phosphorylation promotes H3K27me3 maintenance and epigenetic gene silencing. Phosphorylates CABLES1 (By similarity). Cyclin E/CDK2 prevents oxidative stress-mediated Ras-induced senescence by phosphorylating MYC. Involved in G1-S phase DNA damage checkpoint that prevents cells with damaged DNA from initiating mitosis; regulates homologous recombination-dependent repair by phosphorylating BRCA2, this phosphorylation is low in S phase when recombination is active, but increases as cells progress towards mitosis. In response to DNA damage, double-strand break repair by homologous recombination a reduction of CDK2-mediated BRCA2 phosphorylation. Phosphorylation of RB1 disturbs its interaction with E2F1. NPM1 phosphorylation by cyclin E/CDK2 promotes its dissociates from unduplicated centrosomes, thus initiating centrosome duplication. Cyclin E/CDK2-mediated phosphorylation of NPAT at G1-S transition and until prophase stimulates the NPAT-mediated activation of histone gene transcription during S phase. Required for vitamin D-mediated growth inhibition by being itself inactivated. Involved in the nitric oxide- (NO) mediated signaling in a nitrosylation/activation-dependent manner. USP37 is activated by phosphorylation and thus triggers G1-S transition. CTNNB1 phosphorylation regulates insulin internalization.<ref>PMID:10499802</ref> <ref>PMID:11051553</ref> <ref>PMID:10995386</ref> <ref>PMID:10995387</ref> <ref>PMID:10884347</ref> <ref>PMID:11113184</ref> <ref>PMID:15800615</ref> <ref>PMID:18372919</ref> <ref>PMID:20147522</ref> <ref>PMID:20079829</ref> <ref>PMID:20935635</ref> <ref>PMID:20195506</ref> <ref>PMID:19966300</ref> <ref>PMID:21262353</ref> <ref>PMID:21596315</ref> <ref>PMID:21319273</ref> <ref>PMID:17495531</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cc/2cch_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2cch ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Phospho-CDK2/cyclin A, a kinase that is active in cell cycle S phase, contains an RXL substrate recognition site that is over 40 A from the catalytic site. The role of this recruitment site, which enhances substrate affinity and catalytic efficiency, has been investigated using peptides derived from the natural substrates, namely CDC6 and p107, and a bispeptide inhibitor in which the gamma-phosphate of ATP is covalently attached by a linker to the CDC6 substrate peptide. X-ray studies with a 30-residue CDC6 peptide in complex with pCDK2/cyclin A showed binding of a dodecamer peptide at the recruitment site and a heptapeptide at the catalytic site, but no density for the linking 11 residues. Kinetic studies established that the CDC6 peptide had an 18-fold lower Km compared with heptapeptide substrate and that this effect required the recruitment peptide to be covalently linked to the substrate peptide. X-ray studies with the CDC6 bispeptide showed binding of the dodecamer at the recruitment site and the modified ATP in two alternative conformations at the catalytic site. The CDC6 bispeptide was a potent inhibitor competitive with both ATP and peptide substrate of pCDK2/cyclin A activity against a heptapeptide substrate (Ki = 0.83 nm) but less effective against RXL-containing substrates. We discuss how localization at the recruitment site (KD 0.4 microm) leads to increased catalytic efficiency and the design of a potent inhibitor. The notion of a flexible linker between the sites, which must have more than a minimal number of residues, provides an explanation for recognition and discrimination against different substrates.
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==About this Structure==
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The role of the phospho-CDK2/cyclin A recruitment site in substrate recognition.,Cheng KY, Noble ME, Skamnaki V, Brown NR, Lowe ED, Kontogiannis L, Shen K, Cole PA, Siligardi G, Johnson LN J Biol Chem. 2006 Aug 11;281(32):23167-79. Epub 2006 May 17. PMID:16707497<ref>PMID:16707497</ref>
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2CCH is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with SO4, ATP and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:Gol Binding Site For Chain A'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2CCH OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The role of the phospho-CDK2/cyclin A recruitment site in substrate recognition., Cheng KY, Noble ME, Skamnaki V, Brown NR, Lowe ED, Kontogiannis L, Shen K, Cole PA, Siligardi G, Johnson LN, J Biol Chem. 2006 Aug 11;281(32):23167-79. Epub 2006 May 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16707497 16707497]
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</div>
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[[Category: Homo sapiens]]
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<div class="pdbe-citations 2cch" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Brown, N.R.]]
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[[Category: Cheng, K.Y.]]
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[[Category: Cole, P.A.]]
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[[Category: Johnson, L.N.]]
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[[Category: Kontogiannis, L.]]
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[[Category: Lowe, E.D.]]
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[[Category: Noble, M.E.M.]]
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[[Category: Shen, K.]]
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[[Category: Siligardi, G.]]
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[[Category: Skamnaki, V.]]
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[[Category: ATP]]
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[[Category: GOL]]
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[[Category: SO4]]
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[[Category: atp-binding]]
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[[Category: cdk2]]
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[[Category: cell cycle]]
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[[Category: cell division]]
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[[Category: cyclin]]
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[[Category: mitosis]]
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[[Category: nuclear protein]]
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[[Category: peptide specificity]]
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[[Category: phosphorylation]]
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[[Category: polymorphism]]
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[[Category: protein kinase]]
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[[Category: recruitment]]
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[[Category: serine-threonine-protein kinase]]
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[[Category: serine/threonine-protein kinase]]
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[[Category: transferase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 19:17:34 2007''
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==See Also==
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*[[Cyclin 3D structures|Cyclin 3D structures]]
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*[[Cyclin-dependent kinase 3D structures|Cyclin-dependent kinase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Brown NR]]
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[[Category: Cheng KY]]
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[[Category: Cole PA]]
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[[Category: Johnson LN]]
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[[Category: Kontogiannis L]]
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[[Category: Lowe ED]]
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[[Category: Noble MEM]]
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[[Category: Shen K]]
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[[Category: Siligardi G]]
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[[Category: Skamnaki V]]

Current revision

The crystal structure of CDK2 cyclin A in complex with a substrate peptide derived from CDC modified with a gamma-linked ATP analogue

PDB ID 2cch

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