PDBsum entry 2cn5

Transferase

PDB id

2cn5

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Contents

			Protein chain

					283 a.a. *

			Ligands

					NO3


					ADP

			Metals

					_CL


					_MG ×2

			Waters ×154

* Residue conservation analysis

PDB id:

2cn5

Links

Name:

Transferase

Title:

Crystal structure of human chk2 in complex with adp

Structure:

Serine/threonine-protein kinase chk2. Chain: a. Fragment: kinase domain, residues 210-531. Synonym: chk2, cds1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: human cdna library

Biol. unit:

Dimer (from PDB file)

Resolution:

2.25Å

R-factor:

0.201

R-free:

0.240

Authors:

A.W.Oliver,L.H.Pearl

Key ref:

A.W.Oliver et al. (2006). Trans-activation of the DNA-damage signalling protein kinase Chk2 by T-loop exchange. EMBO J, 25, 3179-3190. PubMed id: 16794575 DOI: 10.1038/sj.emboj.7601209

Date:

18-May-06

Release date:

28-Jun-06

PROCHECK

	Headers

	References

Protein chain

O96017 (CHK2_HUMAN) - Serine/threonine-protein kinase Chk2 from Homo sapiens

Seq: Struc:

Seq: Struc:					543 a.a. 283 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.2.7.11.1 - non-specific serine/threonine protein kinase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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 = ADP) corresponds exactly	+	ADP	+	H(+)

L-threonyl-[protein]	+	ATP	=	O-phospho-L-threonyl-[protein] Bound ligand (Het Group name = ADP) corresponds exactly	+	ADP	+	H(+)

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

reference

DOI no: 10.1038/sj.emboj.7601209	EMBO J 25:3179-3190 (2006)
PubMed id: 16794575

Trans-activation of the DNA-damage signalling protein kinase Chk2 by T-loop exchange.
A.W.Oliver, A.Paul, K.J.Boxall, S.E.Barrie, G.W.Aherne, M.D.Garrett, S.Mittnacht, L.H.Pearl.

ABSTRACT

The protein kinase Chk2 (checkpoint kinase 2) is a major effector of the replication checkpoint. Chk2 activation is initiated by phosphorylation of Thr68, in the serine-glutamine/threonine-glutamine cluster domain (SCD), by ATM. The phosphorylated SCD-segment binds to the FHA domain of a second Chk2 molecule, promoting dimerisation of the protein and triggering phosphorylation of the activation segment/T-loop in the kinase domain. We have now determined the structure of the kinase domain of human Chk2 in complexes with ADP and a small-molecule inhibitor debromohymenialdisine. The structure reveals a remarkable dimeric arrangement in which T-loops are exchanged between protomers, to form an active kinase conformation in trans. Biochemical data suggest that this dimer is the biologically active state promoted by ATM-phosphorylation, and also suggests a mechanism for dimerisation-driven activation of Chk2 by trans-phosphorylation.

Selected figure(s)



	Figure 2. Figure 2 Structure of Chk2 kinase domain. Secondary structure cartoon of the binary complex of CHK2-KD with ADP. The glycine-rich loop is coloured pink, the DFG and APE motifs red, and the T-loop yellow. Secondary structure elements corresponding to -strands are coloured blue and -helices cyan. ADP is shown as a 'stick' model. The catalytic residue Asp347, conserved residues Lys249 and Glu373, and autophosphorylation sites Thr383 and Thr387 are also highlighted. Molecular images in this and subsequent figures were generated using PyMOL (www.pymol.org).		Figure 7. Figure 7 Chk2 T-loop autophosphorylation sites do not resemble endogenous substrates. Alignment of endogenous Chk2 substrate sequences (CDC25A, CDC25C, BRCA-1, E2F-1, PML) with an optimised substrate sequence (Chk2-TIDE) and T-loop autophosphorylation sites. For each sequence, the residue number of the first amino acid is listed (res). The autophosphorylation sites of Chk2 overlap, as indicated by the underlined regions. The 'p' column header indicates the phosphorylated amino acid.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21390216

E.Sala, L.Guasch, J.Iwaszkiewicz, M.Mulero, M.J.Salvadó, M.Pinent, V.Zoete, A.Grosdidier, S.Garcia-Vallvé, O.Michielin, and G.Pujadas (2011).
Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays.

PLoS One, 6, e16903.

21317875

M.M.Ali, T.Bagratuni, E.L.Davenport, P.R.Nowak, M.C.Silva-Santisteban, A.Hardcastle, C.McAndrews, M.G.Rowlands, G.J.Morgan, W.Aherne, I.Collins, F.E.Davies, and L.H.Pearl (2011).
Structure of the Ire1 autophosphorylation complex and implications for the unfolded protein response.

EMBO J, 30, 894-905.

PDB code:

3p23

19854302

J.Eswaran, and S.Knapp (2010).
Insights into protein kinase regulation and inhibition by large scale structural comparison.

Biochim Biophys Acta, 1804, 429-432.

19965870

J.M.Steichen, G.H.Iyer, S.Li, S.A.Saldanha, M.S.Deal, V.L.Woods, and S.S.Taylor (2010).
Global consequences of activation loop phosphorylation on protein kinase A.

J Biol Chem, 285, 3825-3832.

20336692

M.Rabiller, M.Getlik, S.Klüter, A.Richters, S.Tückmantel, J.R.Simard, and D.Rauh (2010).
Proteus in the world of proteins: conformational changes in protein kinases.

Arch Pharm (Weinheim), 343, 193-206.

20462494

P.Barthe, G.V.Mukamolova, C.Roumestand, and M.Cohen-Gonsaud (2010).
The structure of PknB extracellular PASTA domain from mycobacterium tuberculosis suggests a ligand-dependent kinase activation.

Structure, 18, 606-615.

PDB codes:

2kud 2kue 2kuf 2kui

19864428

T.Sunami, N.Byrne, R.E.Diehl, K.Funabashi, D.L.Hall, M.Ikuta, S.B.Patel, J.M.Shipman, R.F.Smith, I.Takahashi, J.Zugay-Murphy, Y.Iwasawa, K.J.Lumb, S.K.Munshi, and S.Sharma (2010).
Structural basis of human p70 ribosomal S6 kinase-1 regulation by activation loop phosphorylation.

J Biol Chem, 285, 4587-4594.

PDB codes:

3a60 3a61 3a62

20713355

X.Guo, M.D.Ward, J.B.Tiedebohl, Y.M.Oden, J.O.Nyalwidhe, and O.J.Semmes (2010).
Interdependent phosphorylation within the kinase domain T-loop Regulates CHK2 activity.

J Biol Chem, 285, 33348-33357.

19741151

A.G.Jobson, G.T.Lountos, P.L.Lorenzi, J.Llamas, J.Connelly, D.Cerna, J.E.Tropea, A.Onda, G.Zoppoli, S.Kondapaka, G.Zhang, N.J.Caplen, J.H.Cardellina, S.S.Yoo, A.Monks, C.Self, D.S.Waugh, R.H.Shoemaker, and Y.Pommier (2009).
Cellular inhibition of checkpoint kinase 2 (Chk2) and potentiation of camptothecins and radiation by the novel Chk2 inhibitor PV1019 [7-nitro-1H-indole-2-carboxylic acid {4-[1-(guanidinohydrazone)-ethyl]-phenyl}-amide].

J Pharmacol Exp Ther, 331, 816-826.

PDB code:

2w7x

19207465

F.A.Pasha, M.Muddassar, and S.Joo Cho (2009).
Molecular docking and 3D QSAR studies of Chk2 inhibitors.

Chem Biol Drug Des, 73, 292-300.

19177354

G.T.Lountos, J.E.Tropea, D.Zhang, A.G.Jobson, Y.Pommier, R.H.Shoemaker, and D.S.Waugh (2009).
Crystal structure of checkpoint kinase 2 in complex with NSC 109555, a potent and selective inhibitor.

Protein Sci, 18, 92.

PDB code:

2w0j

19177573

S.J.Lee, M.H.Cobb, and E.J.Goldsmith (2009).
Crystal structure of domain-swapped STE20 OSR1 kinase domain.

Protein Sci, 18, 304-313.

PDB code:

3dak

19357077

Y.J.Xu, and T.J.Kelly (2009).
Autoinhibition and autoactivation of the DNA replication checkpoint kinase cds1.

J Biol Chem, 284, 16016-16027.

19306398

Y.Li, and A.G.Palmer (2009).
Domain swapping in the kinase superfamily: OSR1 joins the mix.

Protein Sci, 18, 678-681.

19782031

Z.Cai, N.H.Chehab, and N.P.Pavletich (2009).
Structure and activation mechanism of the CHK2 DNA damage checkpoint kinase.

Mol Cell, 35, 818-829.

PDB codes:

3i6u 3i6w

18239682

A.C.Pike, P.Rellos, F.H.Niesen, A.Turnbull, A.W.Oliver, S.A.Parker, B.E.Turk, L.H.Pearl, and S.Knapp (2008).
Activation segment dimerization: a mechanism for kinase autophosphorylation of non-consensus sites.

EMBO J, 27, 704-714.

PDB codes:

2j51 2j7t 2j90 2jfl 2jfm 2uv2

19008858

C.Mieczkowski, A.T.Iavarone, and T.Alber (2008).
Auto-activation mechanism of the Mycobacterium tuberculosis PknB receptor Ser/Thr kinase.

EMBO J, 27, 3186-3197.

PDB codes:

3f61 3f69

18831043

F.Villa, M.Deak, D.R.Alessi, and D.M.van Aalten (2008).
Structure of the OSR1 kinase, a hypertension drug target.

Proteins, 73, 1082-1087.

PDB code:

2vwi

18948271

J.Li, I.A.Taylor, J.Lloyd, J.A.Clapperton, S.Howell, D.Macmillan, and S.J.Smerdon (2008).
Chk2 Oligomerization Studied by Phosphopeptide Ligation: IMPLICATIONS FOR REGULATION AND PHOSPHODEPENDENT INTERACTIONS.

J Biol Chem, 283, 36019-36030.

18566589

J.Wu, W.Li, B.P.Craddock, K.W.Foreman, M.J.Mulvihill, Q.S.Ji, W.T.Miller, and S.R.Hubbard (2008).
Small-molecule inhibition and activation-loop trans-phosphorylation of the IGF1 receptor.

EMBO J, 27, 1985-1994.

PDB code:

3d94

18337243

R.Jacamo, J.Sinnett-Smith, O.Rey, R.T.Waldron, and E.Rozengurt (2008).
Sequential protein kinase C (PKC)-dependent and PKC-independent protein kinase D catalytic activation via Gq-coupled receptors: differential regulation of activation loop Ser(744) and Ser(748) phosphorylation.

J Biol Chem, 283, 12877-12887.

18940813

R.T.Nitta, A.H.Chu, and A.J.Wong (2008).
Constitutive Activity of JNK2{alpha}2 Is Dependent on a Unique Mechanism of MAPK Activation.

J Biol Chem, 283, 34935-34945.

18058223

Z.Kleibl, O.Havranek, J.Novotny, P.Kleiblova, P.Soucek, and P.Pohlreich (2008).
Analysis of CHEK2 FHA domain in Czech patients with sporadic breast cancer revealed distinct rare genetic alterations.

Breast Cancer Res Treat, 112, 159-164.

17627826

A.W.Oliver, S.Knapp, and L.H.Pearl (2007).
Activation segment exchange: a common mechanism of kinase autophosphorylation?

Trends Biochem Sci, 32, 351-356.

17715138

E.M.Kass, J.Ahn, T.Tanaka, W.A.Freed-Pastor, S.Keezer, and C.Prives (2007).
Stability of checkpoint kinase 2 is regulated via phosphorylation at serine 456.

J Biol Chem, 282, 30311-30321.

18004398

L.Antoni, N.Sodha, I.Collins, and M.D.Garrett (2007).
CHK2 kinase: cancer susceptibility and cancer therapy - two sides of the same coin?

Nat Rev Cancer, 7, 925-936.

18077363

O.Fedorov, B.Marsden, V.Pogacic, P.Rellos, S.Müller, A.N.Bullock, J.Schwaller, M.Sundström, and S.Knapp (2007).
A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases.

Proc Natl Acad Sci U S A, 104, 20523-20528.

PDB code:

2j2i

17698850

S.K.Gupta, X.Guo, S.S.Durkin, K.F.Fryrear, M.D.Ward, and O.J.Semmes (2007).
Human T-cell leukemia virus type 1 Tax oncoprotein prevents DNA damage-induced chromatin egress of hyperphosphorylated Chk2.

J Biol Chem, 282, 29431-29440.

17299042

T.Usui, and J.H.Petrini (2007).
The Saccharomyces cerevisiae 14-3-3 proteins Bmh1 and Bmh2 directly influence the DNA damage-dependent functions of Rad53.

Proc Natl Acad Sci U S A, 104, 2797-2802.

16940182

G.Buscemi, L.Carlessi, L.Zannini, S.Lisanti, E.Fontanella, S.Canevari, and D.Delia (2006).
DNA damage-induced cell cycle regulation and function of novel Chk2 phosphoresidues.

Mol Cell Biol, 26, 7832-7845.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.