2.8 References

2.8 References

2.8.1 DDBJ

  • Tateno, Y., T. Imanishi, S. Miyazaki, K. Fukami-Kobayashi, N. Saitou, H. Sugawara, and T. Gojobori. 2002. DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Research 30 (1):27-30.

    Main site

    http://www.ddbj.nig.ac.jp/

    Release notes

    http://www.ddbj.nig.ac.jp/ddbjnew/ddbj_relnote.html

    Download

    ftp://ftp.ddbj.nig.ac.jp/database/ddbj/

2.8.2 EMBL

  • Stoesser, G., W. Baker, A. van den Broek, E. Camon, M. Garcia-Pastor, C. Kanz, T. Kulikova, R. Leinonen, Q. Lin, V. Lombard, R. Lopez, N. Redaschi, P. Stoehr, M. A. Tuli, K. Tzouvara, and R. Vaughan. 2002. The EMBL Nucleotide Sequence Database. Nucleic Acids Research 30 (1):21-26.

    Main page

    http://www.ebi.ac.uk/embl/index.html

    Release notes

    http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.html

    User manual

    http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html

    Download

    ftp://ftp.ebi.ac.uk/pub/databases/embl/

2.8.3 GenBank

  • Benson, D.A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp, and D. L. Wheeler. 2002. GenBank. Nucleic Acids Research 30 (1):17-20.

    GenBank overview

    http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html

    Release notes

    ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt

    Download

    ftp://ftp.ncbi.nih.gov/genbank/

    DDBJ/EMBL/GenBank Feature Table

    http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html

Chapter 3. SWISS-PROT

SWISS-PROT is an annotated protein sequence database that was started in 1986. It is currently overseen by the Swiss Institute of Bioinformatics (SIB) in association with the European Bioinformatics Institute (EBI). SWISS-PROT is the preferred protein sequence database for most bioinformaticians because many of the sequence annotations are curated by scientists. TrEMBL, another sequence database, is a computer-annotated supplement that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT. It has essentially the same sequence flat file format as SWISS-PROT. We're using SWISS-PROT Release 40.

3.1 SWISS-PROT Example Flat File

Example 3-1 contains a sequence entry from SWISS-PROT. This entry contains terms from the SWISS-PROT Field Definitions and Feature Table types, discussed later in this chapter.

Example 3-1. Sample SWISS-PROT sequence entry
ID   CDK2_HUMAN     STANDARD;      PRT;   298 AA.
AC   P24941;
DT   01-MAR-1992 (Rel. 21, Created)
DT   01-AUG-1992 (Rel. 23, Last sequence update)
DT   15-JUN-2002 (Rel. 41, Last annotation update)
DE   Cell division protein kinase 2 (EC 2.7.1.-) (p33 protein kinase).
GN   CDK2.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=91330891; PubMed=1714386;
RA   Elledge S.J., Spottswood M.R.;
RT   "A new human p34 protein kinase, CDK2, identified by complementation
RT   of a cdc28 mutation in Saccharomyces cerevisiae, is a homolog of
RT   Xenopus Eg1.";
RL   EMBO J. 10:2653-2659(1991).
RN   [2]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=91367262; PubMed=1653904;
RA   Tsai L.-H., Harlow E., Meyerson M.;
RT   "Isolation of the human cdk2 gene that encodes the cyclin A- and
RT   adenovirus E1A-associated p33 kinase.";
RL   Nature 353:174-177(1991).
RN   [3]
RP   SEQUENCE FROM N.A.
RX   MEDLINE=92020980; PubMed=1717994;
RA   Ninomiya-Tsuji J., Nomoto S., Yasuda H., Reed S.I., Matsumoto K.;
RT   "Cloning of a human cDNA encoding a CDC2-related kinase by
RT   complementation of a budding yeast cdc28 mutation.";
RL   Proc. Natl. Acad. Sci. U.S.A. 88:9006-9010(1991).
RN   [4]
RP   SEQUENCE FROM N.A.
RC   TISSUE=Placenta;
RA   Strausberg R.;
RL   Submitted (FEB-2001) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   PHOSPHORYLATION SITES.
RX   MEDLINE=93010995; PubMed=1396589;
RA   Gu Y., Rosenblatt J., O'Morgan D.O.;
RT   "Cell cycle regulation of CDK2 activity by phosphorylation of Thr160
RT   and Tyr15.";
RL   EMBO J. 11:3995-4005(1992).
RN   [6]
RP   X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
RX   MEDLINE=93288132; PubMed=8510751;
RA   de Bondt H.L., Rosenblatt J., Jancarik J., Jones H.D.,
RA   Morgan D.O., Kim S.-H.;
RT   "Crystal structure of cyclin-dependent kinase 2.";
RL   Nature 363:595-602(1993).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF COMPLEX WITH CYCLIN A.
RX   MEDLINE=95356811; PubMed=7630397;
RA   Jeffrey P.D., Russo A.A., Polyak K., Gibbs E., Hurwitz J.,
RA   Massague J., Pavletich N.P.;
RT   "Mechanism of CDK activation revealed by the structure of a
RT   cyclinA-CDK2 complex.";
RL   Nature 376:313-320(1995).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (2.33 ANGSTROMS) OF COMPLEX WITH L868276.
RX   MEDLINE=96181476; PubMed=8610110;
RA   de Azevedo W.F. Jr., Muleer-Dieckmann H.-J., Schulze-Gahmen U.,
RA   Worland P.J., Sausville E., Kim S.-H.;
RT   "Structural basis for specificity and potency of a flavonoid
RT   inhibitor of human CDK2, a cell cycle kinase.";
RL   Proc. Natl. Acad. Sci. U.S.A. 93:2735-2740(1996).
RN   [9]
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF COMPLEX WITH CG2A AND KIP1.
RX   MEDLINE=96300318; PubMed=8684460;
RA   Russo A.A., Jeffrey P.D., Patten A.K., Massague J., Pavletich N.P.;
RT   "Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor
RT   bound to the cyclin A-Cdk2 complex.";
RL   Nature 382:325-331(1996).
RN   [10]
RP   X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF COMPLEX WITH CG2A.
RX   MEDLINE=96313126; PubMed=8756328;
RA   Russo A.A., Jeffrey P.D., Pavletich N.P.;
RT   "Structural basis of cyclin-dependent kinase activation by
RT   phosphorylation.";
RL   Nat. Struct. Biol. 3:696-700(1996).
RN   [11]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RX   MEDLINE=97075215; PubMed=8917641;
RA   Schulze-Gahmen U., de Bondt H.L., Kim S.-H.;
RT   "High-resolution crystal structures of human cyclin-dependent kinase
RT   2 with and without ATP: bound waters and natural ligand as guides for
RT   inhibitor design.";
RL   J. Med. Chem. 39:4540-4546(1996).
RN   [12]
RP   X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX   MEDLINE=97475219; PubMed=9334743;
RA   Lawrie A.M., Noble M.E.M., Tunnah P., Brown N.R., Johnson L.N.,
RA   Endicott J.A.;
RT   "Protein kinase inhibition by staurosporine revealed in details of
RT   the molecular interaction with CDK2.";
RL   Nat. Struct. Biol. 4:796-801(1997).
RN   [13]
RP   X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF COMPLEX WITG CKS1.
RX   MEDLINE=96182647; PubMed=8601310;
RA   Bourne Y., Watson M.H., Hickey M.J., Holmes W., Rocque W., Reed S.I.,
RA   Tainer J.A.;
RT   "Crystal structure and mutational analysis of the human CDK2 kinase
RT   complex with cell cycle-regulatory protein CksHs1.";
RL   Cell 84:863-874(1996).
RN   [14]
RP   X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS).
RX   MEDLINE=98342369; PubMed=9677190;
RA   Gray N.S., Wodicka L., Thunnissen A.-M.W.H., Norman T.C., Kwon S.,
RA   Espinoza F.H., Morgan D.O., Barnes G., Leclerc S., Meijer L.,
RA   Kim S.H., Lockhart D.J., Schultz P.G.;
RT   "Exploiting chemical libraries, structure, and genomics in the search
RT   for kinase inhibitors.";
RL   Science 281:533-538(1998).
CC   -!- FUNCTION: PROBABLY INVOLVED IN THE CONTROL OF THE CELL CYCLE.
CC       INTERACTS WITH CYCLINS A, D, OR E. ACTIVITY OF CDK2 IS MAXIMAL
CC       DURING S PHASE AND G2.
CC   -!- ENZYME REGULATION: PHOSPHORYLATION AT THR-14 OR TYR-15 INACTIVATES
CC       THE ENZYME, WHILE PHOSPHORYLATION AT THR-160 ACTIVATES IT.
CC   -!- SIMILARITY: BELONGS TO THE SER/THR FAMILY OF PROTEIN KINASES.
CC       CDC2/CDKX SUBFAMILY.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; X61622; CAA43807.1; -.
DR   EMBL; X62071; CAA43985.1; -.
DR   EMBL; M68520; AAA35667.1; -.
DR   EMBL; BC003065; AAH03065.1; -.
DR   PIR; A41227; A41227.
DR   PIR; S16520; S16520.
DR   PIR; S17873; S17873.
DR   PDB; 1FIN; 27-JAN-97.
DR   PDB; 1HCK; 07-DEC-96.
DR   PDB; 1HCL; 07-DEC-96.
DR   PDB; 1AQ1; 12-NOV-97.
DR   PDB; 1JST; 11-JAN-97.
DR   PDB; 1JSU; 29-JUL-97.
DR   PDB; 1BUH; 09-SEP-98.
DR   PDB; 1B38; 23-DEC-98.
DR   PDB; 1B39; 23-DEC-98.
DR   PDB; 1CKP; 13-JAN-99.
DR   Genew; HGNC:1771; CDK2.
DR   MIM; 116953; -.
DR   InterPro; IPR000719; Euk_pkinase.
DR   InterPro; IPR002290; Ser_thr_pkinase.
DR   Pfam; PF00069; pkinase; 1.
DR   ProDom; PD000001; Euk_pkinase; 1.
DR   SMART; SM00220; S_TKc; 1.
DR   PROSITE; PS00107; PROTEIN_KINASE_ATP; 1.
DR   PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
DR   PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
KW   Transferase; Serine/threonine-protein kinase; ATP-binding;
KW   Cell cycle; Cell division; Mitosis; Phosphorylation; 3D-structure.
FT   DOMAIN        4    286       PROTEIN KINASE.
FT   NP_BIND      10     18       ATP (BY SIMILARITY).
FT   BINDING      33     33       ATP (BY SIMILARITY).
FT   ACT_SITE    127    127       BY SIMILARITY.
FT   MOD_RES      14     14       PHOSPHORYLATION.
FT   MOD_RES      15     15       PHOSPHORYLATION.
FT   MOD_RES     160    160       PHOSPHORYLATION (BY CAK).
FT   MUTAGEN      14     14       T->A: INCREASE ACTIVITY 2 FOLD.
FT   MUTAGEN      15     15       Y->F: INCREASE ACTIVITY 2 FOLD.
FT   MUTAGEN     160    160       T->A: ABOLISHES ACTIVITY.
FT   TURN          2      3
FT   STRAND        4     12
FT   STRAND       17     23
FT   TURN         24     26
FT   STRAND       29     35
FT   HELIX        46     55
FT   TURN         56     57
FT   TURN         61     62
FT   STRAND       63     63
FT   STRAND       66     72
FT   TURN         73     74
FT   STRAND       75     81
FT   STRAND       85     86
FT   HELIX        87     93
FT   TURN         94     97
FT   HELIX       101    120
FT   TURN        121    122
FT   HELIX       130    132
FT   STRAND      133    135
FT   TURN        137    138
FT   STRAND      141    143
FT   TURN        146    147
FT   HELIX       148    151
FT   STRAND      157    157
FT   TURN        159    160
FT   STRAND      163    163
FT   TURN        167    168
FT   HELIX       171    174
FT   TURN        175    176
FT   TURN        182    182
FT   HELIX       183    198
FT   HELIX       208    219
FT   TURN        224    226
FT   TURN        228    229
FT   HELIX       230    232
FT   TURN        234    235
FT   TURN        238    239
FT   HELIX       248    251
FT   TURN        253    254
FT   HELIX       257    266
FT   TURN        267    267
FT   TURN        271    273
FT   HELIX       277    280
FT   TURN        281    282
FT   HELIX       284    286
FT   TURN        287    288
SQ   SEQUENCE   298 AA;  33929 MW;  F90A0F4E70910B51 CRC64;
     MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH
     PNIVKLLDVI HTENKLYLVF EFLHQDLKKF MDASALTGIP LPLIKSYLFQ LLQGLAFCHS
     HRVLHRDLKP QNLLINTEGA IKLADFGLAR AFGVPVRTYT HEVVTLWYRA PEILLGCKYY
     STAVDIWSLG CIFAEMVTRR ALFPGDSEID QLFRIFRTLG TPDEVVWPGV TSMPDYKPSF
     PKWARQDFSK VVPPLDEDGR SLLSQMLHYD PNKRISAKAA LAHPFFQDVT KPVPHLRL

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