Biol. Cell (2005) 97, 113–118 (Printed in Great Britain) Scientiae forum

My Favourite Sites

The Protein Kinase Resource:everything you always wantedto know about protein kinasesbut were afraid to askClotilde Petretti and Claude Prigent1

Groupe Cycle Cellulaire, Equipe labellisee Ligue Nationale Contre le Cancer, UMR 6061 Genetique et Developpement, CNRS,

Universite de Rennes I, IFR 97 Genomique Fonctionnelle et Sante, Faculte de Medecine, 2 avenue du Pr. Leon Bernard, CS 34317,

35043 Rennes cedex, France

AbstractProtein kinases and phosphatases play crucial roles in all the major cellular processes, such as signal transduction,cell differentiation, cell proliferation and cell cycle progression. Protein phosphorylation or dephosphorylation canform the basis of many critical processes, including enzyme activation or inactivation, protein localization andprotein degradation. Given the importance of protein kinases to cellular development and function, it is critical thatthere are effective ways of disseminating information on protein kinases to the research community. This reviewdescribes such a web resource, ‘The Protein Kinase Resource’ (http://pkr.sdsc.edu/html/index.shtml), which servesas a repository for cellular and molecular data on protein kinases.

IntroductionProtein kinases transfer a phosphate, generally fromATP, to protein substrates; but protein phosphoryl-ation is a reversible reaction, phosphatases being thecounterpart enzymes to protein kinases.

Protein kinases form a vast family of enzymes,encoded by more than 500 genes in human cells

1To whom correspondence should be addressed(email claude.prigent@univ-rennes1.fr).Key words: database, genomics, Internet, protein kinase.Abbreviations used: PDB, Protein Data Bank; PKR, The Protein KinaseResource.

(Manning et al., 2002); in comparison, human cellspossess far fewer phosphatase genes, indicating thatprotein kinases have higher substrate specificity.While not all cellular proteins are phosphoproteins,more than 90% are phosphorylated at some point intheir existence, and the phosphorylation status of aprotein depends on the balance between protein kin-ase and phosphatase activities. Perturbation of thisfragile equilibrium can often lead to defects in keycellular mechanisms. Given this vital role in nor-mal cell function and disease, protein kinases form thesecond most important group of proteins consideredas priority targets by pharmaceutical companies forthe design of inhibitors to be used in human therapy.

The organization of protein kinase research beganwhen Hanks et al. (1988) started to classify pro-tein kinases into different families according to their

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sequences, providing a solid basis for a systematic (on-line) representation of the protein kinase family. TheProtein Kinase Resource (PKR) site was founded in1996 as a collaborative project between renowned re-searchers from three major disciplines of importanceto protein kinase research: biology/biochemistry, pro-tein structural chemistryandbiological sequenceanal-ysis (Smith et al., 1997). From 1996 until 1998, PKRwas a complex set of static html pages that offeredvisual representation of the protein kinase structures.Susan Taylor and Lynn F. Ten Eyck were both authorsof the first protein kinase structure [catalytic sub-unit of the cAMP-dependent protein kinase (PKA);Knighton et al., 1991], providing the basis for theProtein Data Base (PDB) format. PDB is a structuralbioinformatics format developed by Lynn F. Ten Eyckand Phil Bourne that became official in 1998 (Bermanet al., 2000). The PKR site evolved to a central data-base, and dynamically generated web content owingto the bioinformatics contributions of Dr MichaelGribskov (San Diego Supercomputer Center, Univer-sity of California San Diego, La Jolla, CA, U.S.A.).In 2001 an improved PKR site was launched byDr Roland Hannes Niedner (San Diego Supercom-puter Center, University of California San Diego,La Jolla, CA, U.S.A.), providing basic proteomicsinformation on more 7000 protein kinase sequencesserved from a database.

‘The Protein Kinase Resource (PKR) aims to be-come a web-accessible compendium of informationon the protein kinase family of enzymes . . . The PKRis a collaborative project of protein kinase researchersand computational biologists working to create adatabase integrating molecular and cellular informa-tion.’

This quote is extracted from the PKR home pageand sums up the PKR’s intent to be a definitive re-source for researchers working on protein kinases, orfor biologists who want to collect information on pro-tein kinases. PKR is a collaborative and interactivesite offering many advantages to the user, includingaccess to a vast quantity of information on proteinkinases, and the possibility of interacting with otherresearchers (mailing lists for example).

PKR: accessibility to a comprehensivedatabaseFour choices are offered to the user wanting to searchthe database. A simple search allows you to find your

Figure 1 First result of a simple search for a term (‘TGFR’in this case)

favourite protein kinase by term, for instance if theusers inputs ‘TGFR’ (transforming growth factor re-ceptor) the search will give eight results (Figure 1).Every result will include a ‘PKR ID’ (html link), thelength in amino acids (aa) of the protein, the mole-cular mass, the isoelectric point (pI) and the species(html link).

The PKR ID is a link to a page of information, itselfcontaining many other links. For instance, the first ofthe eight ‘TGFR’ results corresponds to the TGF-βreceptor type I precursor with 13 cross referencesto other sites such as GenPept, EMBL, TrEMBL,InterPro, FlyBase, PRODOM, PubMed, gi, etc.Checked features can also be displayed either sepa-rately (PROSITE and Pfam) or together using htmlor Java (Figure 2). This window also displays the se-quence of the kinase and the structure, if available,through a PDB search.

The second choice is an advanced search, allowingyou to find your favourite protein kinase by Booleanexpressions such as the source database (PDB, Inter-pret, OMIM, PRODOM, PRINTS, PIR, GenPept,SwissProt, TrEMBL, EMBL, Flybase, DictyDB andPubMed), name and/or annotation. For example, with‘EMBL accession number D25540’ and ‘TGFR’ theadvanced search will provide one result with the samefeatures as found with the simple search (PKR ID,length, molecular mass, isoelectric point and species).

Lastly, when the proteomics analysis has been re-alised and when only the protein sequence, the iso-electric point or the molecular mass of the unknownprotein kinase is available, two other choices areoffered. A classic ‘sequence search’ using the proteinsequence can be performed, or a ‘proteomics search’using the isoelectric point and/or molecular mass. Theresults are displayed in the same way (PKR ID, lengthetc.). Morever, when available, the protein structure

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The Protein Kinase Resource Scientiae forum

Figure 2 PKR ID information link

can be obtained with its subdomains. For illustration,Figure 3(A) shows the three-dimensional structure ofthe cytoplasmic domain of the type I TGF-receptorand its protein sequence.

For every kinase the same subdomains are sym-bolized by the same colour in the three-dimensionalstructure and in the protein sequence. One sub-domain can then be selected, for instance ‘the redsubdomain of cytoplasmic domain of the type I TGF-receptor’, and the sequence appears underlined andoverlined in white (Figure 3B). The location of thissubdomain in the structure is shown in the sameway as the subdomain I of cytoplasmic domain of thetype I TGF-receptor. The associated protein sequenceappears in white in the upper right-hand corner of thewindow, with kinase-conserved amino acids shown inred (Figure 3C). In addition, if the structure of yourprotein kinase is unknown, it can be analysed usinga ‘predict protein server’ by submitting your proteinsequence by email.

Finally, information on diseases associated withgenetic defects in your favourite protein kinase isoffered on the PKR website. A list of protein kinasesimplicated in diseases is clustered with their NCBI

Figure 3 Three-dimensional protein structure(A) Whole protein. (B) Subdomain selection (under/overlined

sequence). (C) Selected subdomain structure and sequence

(with whole protein inset).

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Figure 4 NCBI website link

accession numbers. For example, information on dis-eases caused by defects in ‘TGF-β type I receptor’ areaccessible through a link to the NCBI website using‘the kinase accession number 190181’ (Figure 4). Theresult will appear with the gene map locus, an explan-atory text about various cloned forms, their features,their protein functions, the genetic defects associated,and linked references. For instance, two TGFR formsexist: TGFR type I and type II. The TGFRI gene isapprox. 31 kb long, contains nine exons and is locatedon 9q33–q34. TGFRI is a 70 kDa protein, is a serine/threonine kinase and its catalytic domain is containedin the C-terminal portion of the protein. TGF-β isthe natural substrate of TGFRI and TGF-β stim-ulation leads to SMAD protein phosphorylation,allowing transcription of target genes. Finally, gen-etic defects in TGFRI lead to defects in angiogen-esis, functional haematopoiesis and vascular defectsin vivo.

PKR: interactivity of repositoryAs well as the database, several other types of in-formation can be found on the website. Firstly, re-

commended protocols are proposed on the PKR site.One can collect information and advice on kinaseactivity assays, purification of recombinant enzymes,peptide mapping, phosphoamino acid analysis,physico-chemical characterization and protein phos-phorylation protocols provided by various research-ers. In this way anyone can also add their specificprotocols or advice on the site, allowing for inter-activity between kinase researchers.

Secondly, advertisements for conferences and meet-ings on protein kinases can be posted on the site,with dates and corresponding links to informationabout the meeting agenda and registration details(Figure 5).

Thirdly, presentations on and links to various biol-ogy education subjects such as ‘what is a protein?’,‘primers in biology’ or ‘protein kinases and cell sig-nalling technology’ are proposed and posted on thesite.

Lastly, the PKR site allows direct interaction withother kinase researchers. Indeed, there is a compre-hensive listing of people involved in protein kinaseresearch and related investigation, with their email

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Figure 5 Links to protein-kinase-related upcoming events

addresses. Anybody can subscribe to a PKR mailinglist by simply sending an email to kinases@sdsc.edu.This mailing list allows the free diffusion of ideas,advice or comments between researchers, from stu-dents to senior researchers. Specific questions can besent to the PKR mailing list; for example, if one islooking for an antibody he/she will receive answersfrom not only other investigators but also privatecompanies. Anything you always wanted to know

about protein kinases can be asked! Researchers inthe field will propose many solutions.

To conclude, http://pkr.sdsc.edu/html/index.shtml is THE web site for research investigatorsworking on protein kinases.

Oleksandr Buzko, who has been developing thePKR Explorer (a Java-based three-dimensional visu-alization application designed to provide a graphicalinterface to access the data available from the PKR

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Figure 6 PKR site improvements are in progress

database since 2003), is currently renovating the site.However, the main organization is conserved. Thefirst page will soon appear as shown in Figure 6.

AcknowledgementsWe wish to thank Dr R. Hannes Niedner, PKR Pro-ject Manager and Technical Lead, for allowing us touse extracts of the PKR Web site, and Dr KevinEliceiri for proofreading the manuscript before sub-mission. We are also grateful to the Ligue NationalContre le Cancer for financial support (equipe label-lisee). Clotilde Petretti is the recipient of a fellowshipfrom the Region Bretagne.

ReferencesBerman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N.,

Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The ProteinData Bank. Nucleic Acids Res. 28, 235–242

Hanks, S.K., Quinn, A.M. and Hunter, T. (1988) The protein kinasefamily: conserved features and deduced phylogeny of the catalyticdomains. Science (Washington, D.C.) 241, 42–52

Knighton, D.R., Zheng, J.H., Ten Eyck, L.F., Ashford, V.A., Xuong,N.H., Taylor, S.S. and Sowadski, J.M. (1991) Crystal structure ofthe catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science (Washington, D.C.) 253,407–414

Manning, G., Whyte, D.B., Martinez, R., Hunter, T. andSudarsanam, S. (2002) The protein kinase complement of thehuman genome. Science (Washington, D.C.) 298, 1912–1934

Smith, C.M., Shindyalov, I.N., Veretnik, S., Gribskov, M., Taylor, S.S.,Ten Eyck, L.F. and Bourne, P.E. (1997) The Protein KinaseResource. Trends Biochem. Sci. 22, 444–446

Received 24 June 2004; accepted 29 July 2004

Published on the Internet 21 January 2005, DOI 10.1042/BC20040077

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