Crystal Structure of Human Cyclin K, a Positive Regulator of Cyclin-dependent Kinase 9

Baek, Kwang Je; Brown, Raymond S.; Birrane, Gabriel; Ladias, John A. A.

doi:10.1016/j.jmb.2006.11.057

Cited by 27 publications

(26 citation statements)

References 63 publications

(19 reference statements)

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“…Our data indicate that the different chemical nature of the interface relates primarily to the preferential binding of cyclin K to CDK12 or CDK13. This is important since inhibitors that interfere with CDK9/cyclin T1 or CDK9/cyclin K binding or P-TEFb kinase activity are being pursued for therapeutic applications in AIDS, heart hypertrophy, and cancer (2,52). Our data suggest that CDK9-, cyclin K-, and PTEFb-based inhibitors may also modulate functions associated with CDK12 or CDK13.…”

Section: Discussionmentioning

confidence: 82%

Interaction of Cyclin-Dependent Kinase 12/CrkRS with Cyclin K1 Is Required for the Phosphorylation of the C-Terminal Domain of RNA Polymerase II

Cheng

Kuzyk

Moradian

et al. 2012

Molecular and Cellular Biology

101

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e CrkRS (Cdc2-related kinase, Arg/Ser), or cyclin-dependent kinase 12 (CKD12), is a serine/threonine kinase believed to coordinate transcription and RNA splicing. While CDK12/CrkRS complexes were known to phosphorylate the C-terminal domain (CTD) of RNA polymerase II (RNA Pol II), the cyclin regulating this activity was not known. Using immunoprecipitation and mass spectrometry, we identified a 65-kDa isoform of cyclin K (cyclin K1) in endogenous CDK12/CrkRS protein complexes. We show that cyclin K1 complexes isolated from mammalian cells contain CDK12/CrkRS but do not contain CDK9, a presumed partner of cyclin K. Analysis of extensive RNA-Seq data shows that the 65-kDa cyclin K1 isoform is the predominantly expressed form across numerous tissue types. We also demonstrate that CDK12/CrkRS is dependent on cyclin K1 for its kinase activity and that small interfering RNA (siRNA) knockdown of CDK12/CrkRS or cyclin K1 has similar effects on the expression of a luciferase reporter gene. Our data suggest that cyclin K1 is the primary cyclin partner for CDK12/CrkRS and that cyclin K1 is required to activate CDK12/CrkRS to phosphorylate the CTD of RNA Pol II. These properties are consistent with a role of CDK12/CrkRS in regulating gene expression through phosphorylation of RNA Pol II.

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Section: Discussionmentioning

confidence: 82%

Interaction of Cyclin-Dependent Kinase 12/CrkRS with Cyclin K1 Is Required for the Phosphorylation of the C-Terminal Domain of RNA Polymerase II

Cheng

Kuzyk

Moradian

et al. 2012

Molecular and Cellular Biology

101

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“…Low-density lipoprotein receptor -related protein 12, also known as suppressor of tumorigenicity protein 7, a tumor suppressive protein whose gene is located on human chromosome 8 q22.2-23.1, a locus of high polymorphism and genetic alterations in cancer biopsies including HNSCC (29), was only found in normal oral epithelium. Similarly, a single peptide for cyclin K, a protein that acts as a regulatory subunit of CDK9 thereby regulating the transcription of a subset of genes (30), was detected only in normal tissues. As cyclin K is regulated by p53, its loss in tumor tissues may reflect the decreased p53 activity that characterizes HNSCC (3).…”

Section: Discussionmentioning

confidence: 99%

Proteomic Analysis of Laser-Captured Paraffin-Embedded Tissues: A Molecular Portrait of Head and Neck Cancer Progression

Patel

Hood

Molinolo

et al. 2008

Clinical Cancer Research

188

151

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Purpose: Squamous cell carcinoma of the head and neck (HNSCC), the sixth most prevalent cancer among men worldwide, is associated with poor prognosis, which has improved only marginally over the past three decades. A proteomic analysis of HNSCC lesions may help identify novel molecular targets for the early detection, prevention, and treatment of HNSCC. Experimental Design: Laser capture microdissection was combined with recently developed techniques for protein extraction from formalin-fixed paraffin-embedded (FFPE) tissues and a novel proteomics platform. Approximately 20,000 cells procured from FFPE tissue sections of normal oral epithelium and well, moderately, and poorly differentiated HNSCC were processed for mass spectrometry and bioinformatic analysis. Results: A large number of proteins expressed in normal oral epithelium and HNSCC, including cytokeratins, intermediate filaments, differentiation markers, and proteins involved in stem cell maintenance, signal transduction, migration, cell cycle regulation, growth and angiogenesis, matrix degradation, and proteins with tumor suppressive and oncogenic potential, were readily detected. Of interest, the relative expression of many of these molecules followed a distinct pattern in normal squamous epithelia and well, moderately, and poorly differentiated HNSCC tumor tissues. Representative proteins were further validated using immunohistochemical studies in HNSCC tissue sections and tissue microarrays. Conclusions: The ability to combine laser capture microdissection and in-depth proteomic analysis of FFPE tissues provided a wealth of information regarding the nature of the proteins expressed in normal squamous epithelium and during HNSCC progression, which may allow the development of novel biomarkers of diagnostic and prognostic value and the identification of novel targets for therapeutic intervention in HNSCC.

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“…CycK and CycT1 have 53 identical residues in the cyclin homology box domain, which is responsible for binding to CDK9 (44); hence, the possibility of competition between CycK and CycT1 for binding to CDK9 cannot be ruled out. The Tat-interacting region, also known as the Tat-responsive motif, located outside the cyclin homology box of CycT1, is not present in CycK (49,50), and thus a possible role of the CDK9-CycK complex in modulating HIV-1 transcription can be ruled out.…”

Section: Discussionmentioning

confidence: 99%

“…The five helices comprising the N-and C-terminal cyclin domains are designated as H1-H5 and H1Ј-H5Ј, respectively. The N-terminal domain (amino acids 1-151) of CycK is responsible for binding to CDK9; however, the two N-terminal helices HNa and HNb are not essential (44). The region from amino acids 152 to 267 forms cyclin box 2, and the region comprising amino acids 268 -354 can be considered as the C terminus of the protein (Fig.…”

Section: Cyclin Box 1 Is Required For Cyck-mediated Reduction Of Ltr-mentioning

confidence: 99%

“…Nef Induces Cyclin K Interaction with CDK9-The CDK9-CycT1 complex (P-TEFb complex) plays a central role in HIV-1 LTR-driven gene expression (46). Both CycK and CycT1 are known to bind CDK9 through their N-terminal cyclin box of which 53 of 80 residues are identical (17,44). Based on this report, we initiated studies to elucidate the mechanism of CycK-mediated reduction in viral gene expression.…”

Section: Cyclin Box 1 Is Required For Cyck-mediated Reduction Of Ltr-mentioning

confidence: 99%

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Cyclin K Inhibits HIV-1 Gene Expression and Replication by Interfering with Cyclin-dependent Kinase 9 (CDK9)-Cyclin T1 Interaction in Nef-dependent Manner

Khan

Mitra

2011

Journal of Biological Chemistry

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Human immunodeficiency virus type-1 (HIV-1) perpetuates its survival in the host by utilizing multiple strategies such as irreversible integration of its DNA into the host cell genome to establish the provirus (1), diversification of its genome to escape or tolerate adaptive immune responses (2), and use of the accessory genes (nef, vif, vpu, and vpr) to modulate host cell immune responses further (3-5). These viral accessory genes are frequently seen as dispensable in many in vitro cell culture systems but seem to be indispensable, in the context of natural infections in vivo. Among these accessory genes, pleiotropic functions of Nef have been studied extensively. It is a 27-30-kDa, N-terminally myristoylated protein having a well characterized CD4 down-regulatory activity (6). Nef does not possess any enzymatic activity, but it modulates diverse signaling pathways and the gene expression of host cell proteins (7,8). Furthermore, Nef influences the activation state of the host cell by bringing together different host cell proteins, protein kinases, and components of the endocytic machinery and making the cells permissible to the virus (9, 10). All these functions of Nef are manifested by a number of events such as activation of signaling molecules, modulation of apoptosis, activation of transcription factors, mitigation of transcriptional repressors, and an increase in the infectivity of virions (11). Although these functions of Nef have been well studied, controversy exists on its role in viral infectivity and replication as both negative (12, 13) and positive (14, 15) roles have been attributed in the literature. Although a number of reports show that Nef increases viral replication by activating T-cells, the molecular basis of Nef-induced viral gene expression and replication remains to be clearly elucidated. Nef was also shown to physically interact with Tat and augment viral gene expression (16), although availability of Tat is critical for the elongation step of long terminal repeat (LTR) 2 -driven transcription by RNA polymerase II. Several cellular factors have been identified for their roles in this process, including positive transcription elongation factor b (P-TEFb) complex. Different P-TEFb complexes isolated from mammalian cells contain a common catalytic subunit, cyclin-dependent kinase 9 (CDK9), and one of the regulatory cyclins, CycT1, CycT2a, CycT2b,. However, CycT1-containing P-TEFb complex is the key complex responsible for HIV-1 transcription elongation (19). Tat is expressed early in the replicative cycle of HIV and is essential for viral gene expression from the LTR promoter. It recognizes the 5Ј-bulge in the transactivation response stem loop RNA, which is located at the 5Ј-end of all viral transcripts. Tat binds to CycT1, and together they form the combinatorial surface that interacts with the transactivation response RNA with high affinity and specificity. The obligate partner of CycT1, CDK9, then hyperphosphorylates the C-terminal domain (CTD) of RNA polymerase II, resulting in incre...

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Crystal Structure of Human Cyclin K, a Positive Regulator of Cyclin-dependent Kinase 9

Cited by 27 publications

References 63 publications

Interaction of Cyclin-Dependent Kinase 12/CrkRS with Cyclin K1 Is Required for the Phosphorylation of the C-Terminal Domain of RNA Polymerase II

Interaction of Cyclin-Dependent Kinase 12/CrkRS with Cyclin K1 Is Required for the Phosphorylation of the C-Terminal Domain of RNA Polymerase II

Proteomic Analysis of Laser-Captured Paraffin-Embedded Tissues: A Molecular Portrait of Head and Neck Cancer Progression

Cyclin K Inhibits HIV-1 Gene Expression and Replication by Interfering with Cyclin-dependent Kinase 9 (CDK9)-Cyclin T1 Interaction in Nef-dependent Manner

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