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 //

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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