PDBsum entry 4cxa

Transferase

PDB id: 4cxa

Contents

Protein chains

330 a.a.

246 a.a.

Ligands

ANP

PDB id:

4cxa

Name:

Transferase

Title:

Crystal structure of the human cdk12-cyclin k complex bound to amppnp

Structure:

Cyclin-dependent kinase 12. Chain: a, c. Fragment: kinase domain, residues 715-1052. Synonym: cdc2-related kinase, arginine/serine-rich, crkrs, cell division cycle 2-related protein kinase 7, cdc2-related protein kinase 7, cell division protein kinase 12, hcdk12, cdk12. Engineered: yes. Cyclin-k. Chain: b, d.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9.

Resolution:

3.15Å R-factor: 0.224 R-free: 0.279

Authors:

S.E.Dixon Clarke,J.M.Elkins,A.C.W.Pike,R.Nowak,S.Goubin,R.P.Mahajan, J.Kopec,S.Froese,C.Tallant,E.P.Carpenter,A.Mackenzie,B.Faust, N.Burgess-Brown,F.Von Delft,C.Arrowsmith,A.M.Edwards,C.Bountra, A.Bullock

Key ref:

S.E.Dixon-Clarke et al. (2015). Structures of the CDK12/CycK complex with AMP-PNP reveal a flexible C-terminal kinase extension important for ATP binding. Sci Rep, 5, 17122. PubMed id: 26597175 DOI: 10.1038/srep17122

Date:

04-Apr-14 Release date: 21-May-14

Protein chains

Q9NYV4  (CDK12_HUMAN) -  Cyclin-dependent kinase 12 from Homo sapiens

Seq: 1490 a.a.

Struc: 330 a.a.*

Protein chains

O75909  (CCNK_HUMAN) -  Cyclin-K from Homo sapiens

Seq: 580 a.a.

Struc: 246 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: Chains A, C: 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⁺

L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + ADP + H(+)

L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + ADP + H(+)

• Enzyme class 3: Chains A, C: E.C.2.7.11.23 - [RNA-polymerase]-subunit kinase.
• Reaction: [DNA-directed RNA polymerase] + ATP = phospho-[DNA-directed RNA polymerase] + ADP + H⁺

[DNA-directed RNA polymerase] + ATP = phospho-[DNA-directed RNA polymerase] (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + ADP + H(+)

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: 10.1038/srep17122

Sci Rep 5:17122 (2015)

PubMed id: 26597175

Structures of the CDK12/CycK complex with AMP-PNP reveal a flexible C-terminal kinase extension important for ATP binding.

S.E.Dixon-Clarke, J.M.Elkins, S.W.Cheng, G.B.Morin, A.N.Bullock.

ABSTRACT

Cyclin-dependent kinase 12 (CDK12) promotes transcriptional elongation by phosphorylation of the RNA polymerase II C-terminal domain (CTD). Structure-function studies show that this activity is dependent on a C-terminal kinase extension, as well as the binding of cyclin K (CycK). To better define these interactions we determined the crystal structure of the human CDK12/CycK complex with and without the kinase extension in the presence of AMP-PNP. The structures revealed novel features for a CDK, including a large β4-β5 loop insertion that contributes to the N-lobe interaction with the cyclin. We also observed two different conformations of the C-terminal kinase extension that effectively open and close the ATP pocket. Most notably, bound AMP-PNP was only observed when trapped in the closed state. Truncation of this C-terminal structure also diminished AMP-PNP binding, as well as the catalytic activity of the CDK12/CycK complex. Further kinetic measurements showed that the full length CDK12/CycK complex was significantly more active than the two crystallised constructs suggesting a critical role for additional domains. Overall, these results demonstrate the intrinsic flexibility of the C-terminal extension in CDK12 and highlight its importance for both ATP binding and kinase activity.