PDBsum entry 6t41

Transcription

PDB id: 6t41

Contents

Protein chains

346 a.a.

267 a.a.

Ligands

MFE

EDO

FMT ×5

Waters ×144

PDB id:

6t41

Name:

Transcription

Title:

Cdk8/cyclin c in complex with n-(4-chlorobenzyl)isoquinolin-4-amine

Structure:

Cyclin-dependent kinase 8. Chain: a. Synonym: cell division protein kinase 8,mediator complex subunit cdk8,mediator of RNA polymerase ii transcription subunit cdk8,protein kinase k35. Engineered: yes. Cyclin-c. Chain: b. Synonym: srb11 homolog,hsrb11.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cdk8. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: ccnc. Expression_system_taxid: 7108

Resolution:

2.45Å R-factor: 0.185 R-free: 0.256

Authors:

E.V.Schneider,K.Maskos,R.Huber,C.-D.Kuhn

Key ref:

F.Klatt et al. (2020). A precisely positioned MED12 activation helix stimulates CDK8 kinase activity. Proc Natl Acad Sci U S A, 117, 2894-2905. PubMed id: 31988137 DOI: 10.1073/pnas.1917635117

Date:

11-Oct-19 Release date: 01-Jan-20

Protein chain

P49336  (CDK8_HUMAN) -  Cyclin-dependent kinase 8 from Homo sapiens

Seq: 464 a.a.

Struc: 346 a.a.

Protein chain

P24863  (CCNC_HUMAN) -  Cyclin-C from Homo sapiens

Seq: 283 a.a.

Struc: 267 a.a.

Enzyme reactions

• Enzyme class 1: Chain A: E.C.2.7.11.22 - cyclin-dependent kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺
• Enzyme class 2: Chain A: E.C.2.7.11.23 - [RNA-polymerase]-subunit kinase.
• Reaction: [DNA-directed RNA polymerase] + ATP = phospho-[DNA-directed RNA polymerase] + ADP + H⁺
• Enzyme class 3: Chain B: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1917635117

Proc Natl Acad Sci U S A 117:2894-2905 (2020)

PubMed id: 31988137

A precisely positioned MED12 activation helix stimulates CDK8 kinase activity.

F.Klatt, A.Leitner, I.V.Kim, H.Ho-Xuan, E.V.Schneider, F.Langhammer, R.Weinmann, M.R.Müller, R.Huber, G.Meister, C.D.Kuhn.

ABSTRACT

The Mediator kinase module regulates eukaryotic transcription by phosphorylating transcription-related targets and by modulating the association of Mediator and RNA polymerase II. The activity of its catalytic core, cyclin-dependent kinase 8 (CDK8), is controlled by Cyclin C and regulatory subunit MED12, with its deregulation contributing to numerous malignancies. Here, we combine in vitro biochemistry, cross-linking coupled to mass spectrometry, and in vivo studies to describe the binding location of the N-terminal segment of MED12 on the CDK8/Cyclin C complex and to gain mechanistic insights into the activation of CDK8 by MED12. Our data demonstrate that the N-terminal portion of MED12 wraps around CDK8, whereby it positions an "activation helix" close to the T-loop of CDK8 for its activation. Intriguingly, mutations in the activation helix that are frequently found in cancers do not diminish the affinity of MED12 for CDK8, yet likely alter the exact positioning of the activation helix. Furthermore, we find the transcriptome-wide gene-expression changes in human cells that result from a mutation in the MED12 activation helix to correlate with deregulated genes in breast and colon cancer. Finally, functional assays in the presence of kinase inhibitors reveal that binding of MED12 remodels the active site of CDK8 and thereby precludes the inhibition of ternary CDK8 complexes by type II kinase inhibitors. Taken together, our results not only allow us to propose a revised model of how CDK8 activity is regulated by MED12, but also offer a path forward in developing small molecules that target CDK8 in its MED12-bound form.