Editing Cyclin-dependent kinase complex (section)

== Structure and Regulation ==
[[File:Two steps in Cdk activation.pdf|thumb|Cyclin binding alone causes partial activation of Cdks, but complete activation also requires activating phosphorylation by CAK. In animal cells, CAK phosphorylates the Cdk subunit only after cyclin binding, and so the two steps in Cdk activation are usually ordered as shown here, with cyclin binding occurring first. Budding yeast contains a different version of CAK that can phosphorylate the Cdk even in the absence of cyclin, and so the two activation steps can occur in either order. In all cases, CAK tends to be in constant excess in the cell, so that cyclin binding is the rate-limiting step in Cdk activation.]]

[[File:Substrate-targeting sites on cyclin–Cdk complexes.pdf|thumb|The central substrate-recognition site on Cdks lies in the active-site T-loop, which interacts with the SPXK consensus sequence that contains the phosphorylation site (see Figure 3-12). An RXL motif in some substrates interacts with the hydrophobic patch on the cyclin, thereby enhancing the rate of phosphorylation. The presence of a phosphate-binding pocket on the accessory subunit Cks1 may facilitate interactions with targets that contain multiple phosphorylation sites.]]

The structure of [[Cyclin-dependent kinase|CDKs]] in complex with a cyclin subunits (CDKC) has long been a goal of structural and cellular biologists starting in the 1990s when the structure of unbound cyclin A was solved by Brown et al. and in the same year Jeffery et al. solved the structure of human cyclin A-CDK2 complex to 2.3 Angstrom resolution.<ref name=":0">Kristi Levine, Frederick R Cross, Structuring cell-cycle biology, Structure, Volume 3, Issue 11, 1995, Pages 1131-1134, ISSN 0969-2126, {{doi|10.1016/S0969-2126(01)00248-9}}.</ref> Since this time, many CDK structures have been determined to higher resolution, including the structures of CDK2 and CDK2 bound to a variety of substrates, as seen in Figure 1.
High resolution structures exist for approximately 25 CDK-cyclin complexes in total within the [[Protein Data Bank]].<ref name=":1">Wood, D. J., & Endicott, J. A. (2018). Structural insights into the functional diversity of the CDK-cyclin family. Open biology, 8(9), 180112.</ref> Based on function, there are two general populations of CDK-cyclin complex structures, open and closed form. The difference between the forms lies within the binding of cyclin partners where closed form complexes have CDK-cyclin binding at both the C and N-termini of the activation loop of the CDK, whereas the open form partners bind only at the N-terminus. Open form structures correspond most often to those complexes involved in transcriptional regulation (CDK 8, 9, 12, and 13), while closed form CDK-cyclin complex are most often involved in cell cycle progression and regulation (CDK 1, 2, 6). These distinct roles, however, do not significantly differ with the sequence homology between the CDK components. In particular, among these known structures there appear to be four major conserved regions: a N-terminal Glycine-rich loop, a Hinge Region, an αC-helix, and a T-loop regulation site.<ref name=":1" />

=== Activation Loop ===
The [[activation loop]], also referred to as the T-loop, is the region of CDK (between the DFG and APE motifs in many CDK)<ref name=":1" /> that is enzymatically active when CDK is bound to its function-specific partner. In CDK-cyclin complexes, this activation region is composed of a conserved αL-12 Helix and contains a key phosphorylatable residue (usually [[Amino acid|Threonine]] for CDK-cyclin partners, but also includes Serine and Tyrosine) that mediates the enzymatic activity of the CDK. It is at this essential residue (T160 in CDK2 complexes, T177 in CDK6 complexes) that enzymatic ATP-phosphorylation of CDK-cyclin complexes by CAK (cyclin activating kinase, referring to the CDK7-Cyclin H complex in human cells) takes place. After the hydrolysis of ATP to phosphorylate at this site, these complexes are able to complete their intended function, the phosphorylation of cellular targets. It is important to note that in CDK 1, 2 and 6, the T-loop and a separate C-terminal region are the major sites of cyclin binding in the CDK, and which cyclins are bound to each of these CDK is mediated by the particular sequence of the activation site T-loop. These cyclin binding sites are the regions of highest variability in CDKs despite relatively high sequence homology surrounding the αL-12 Helix motif of this structural component.<ref name=":1" />

=== Glycine-rich region ===
The [[glycine]]-rich loop (Gly-rich loop) as seen in residues 12-16 in CDK2 encodes a conserved GXGXXG motif across both yeast and animal models. The regulatory region is subject to differential phosphorylation at non-glycine residues within this motif, making this site subject to [[Wee1]] and/or [[MYT1|Myt1]] inhibitory kinase phosphorylation and [[Cdc25]] de-phosphorylation in mammals. This reversible phosphorylation at the Gly-rich loop in CDK2 occurs at Y15, where activity has been further studied. Study of this residue has shown that phosphorylation promotes a conformational change that prevents ATP and substrate binding by steric interference with these necessary binding sites in the activation loop of the CDK-cyclin complexes. This activity is aided by the notable flexibility that the Gly-rich loop has within the structure of most CDK allowing for its rotation toward the activation loop to have a significant effect on reducing substrate affinity without major changes in the overall CDK-cyclin complex structure.<ref name=":0" /><ref>Malumbres: Cyclin-dependent kinases. ''Genome Biology,'' 2014, 15:22, {{doi|10.1186/gb4184}}</ref>

=== Hinge Region ===
The conserved hinge region of CDK within eukaryotic cells acts as an essential bridge between the Gly-rich loop and the activation loop. CDK are characterized by a N-terminal lobe that is primarily twisted beta-sheet connected via this hinge region to an alpha helix dominated C-terminal lobe. In discussion of the T-loop and the Gly-rich loop, it is important to note that these regions, which must be able to spatially interact in order to carry out their biochemical functions, lie on opposite lobes of the CDK itself. Thus, this hinge region, which can vary in length slightly between CDK type and CDK-cyclin complex, connects essential regulatory regions of the CDK by connecting these lobes, and plays key roles in the resulting structure of CDK-cyclin complexes by properly orienting ATP for easy catalysis of phosphorylation reactions by the assembled complex. <ref name=":0" /><ref name=":1" />

=== αC-Helix ===
The αC-Helix region is highly conserved across many of the mammalian kinome (family of [[Kinase|kinases]]). Its main responsibility is to maintain [[Allosteric regulation|allosteric control]] of the kinase active site. This control manifests in CDK-cyclin complexes by specifically preventing CDK activity until its binds to its partner regulator (i.e. cyclin or other partner protein). This binding causes a conformational change in the αC-Helix region of the CDK and allows for it to be moved from the active site cleft and completes the initial process of T-loop activation. Given that this region is so conserved across the protein superfamily of kinases, this mechanism where the αC-Helix has been shown to fold out of the N-terminal lobe of the kinase, allowing for increased access to the αL-12 Helix that lies within the T-loop, is considered a potential target for drug development.<ref>Lorenzo Palmieri, Giulio Rastelli, αC helix displacement as a general approach for allosteric modulation of protein kinases, Drug Discovery Today, Volume 18, Issues 7–8, 2013, Pages 407-414, ISSN 1359-6446, {{doi|10.1016/j.drudis.2012.11.009}}.</ref>