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VINT_LAMBD
ID   VINT_LAMBD              Reviewed;         356 AA.
AC   P03700;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   21-JUL-1986, sequence version 1.
DT   23-FEB-2022, entry version 142.
DE   RecName: Full=Integrase;
DE            EC=2.7.7.- {ECO:0000269|PubMed:15973401};
DE            EC=3.1.-.- {ECO:0000269|PubMed:15973401};
GN   Name=int;
OS   Escherichia phage lambda (Bacteriophage lambda).
OC   Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC   Caudovirales; Siphoviridae; Lambdavirus.
OX   NCBI_TaxID=10710;
OH   NCBI_TaxID=562; Escherichia coli.
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=6221115; DOI=10.1016/0022-2836(82)90546-0;
RA   Sanger F., Coulson A.R., Hong G.F., Hill D.F., Petersen G.B.;
RT   "Nucleotide sequence of bacteriophage lambda DNA.";
RL   J. Mol. Biol. 162:729-773(1982).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=6446713; DOI=10.1073/pnas.77.5.2482;
RA   Hoess R.H., Foeller C., Bidwell K., Landy A.;
RT   "Site-specific recombination functions of bacteriophage lambda: DNA
RT   sequence of regulatory regions and overlapping structural genes for Int and
RT   Xis.";
RL   Proc. Natl. Acad. Sci. U.S.A. 77:2482-2486(1980).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=6253947; DOI=10.1093/nar/8.8.1765;
RA   Davies R.W.;
RT   "DNA sequence of the int-xis-Pi region of the bacteriophage lambda; overlap
RT   of the int and xis genes.";
RL   Nucleic Acids Res. 8:1765-1782(1980).
RN   [4]
RP   INTERACTION WITH THE EXCISIONASE, AND MUTAGENESIS OF GLU-47.
RX   PubMed=12832614; DOI=10.1073/pnas.1033041100;
RA   Warren D., Sam M.D., Manley K., Sarkar D., Lee S.Y., Abbani M.,
RA   Wojciak J.M., Clubb R.T., Landy A.;
RT   "Identification of the lambda integrase surface that interacts with Xis
RT   reveals a residue that is also critical for Int dimer formation.";
RL   Proc. Natl. Acad. Sci. U.S.A. 100:8176-8181(2003).
RN   [5]
RP   REVIEW, AND FUNCTION.
RX   PubMed=16139195; DOI=10.1016/j.cub.2005.08.031;
RA   Van Duyne G.D.;
RT   "Lambda integrase: armed for recombination.";
RL   Curr. Biol. 15:R658-R660(2005).
RN   [6]
RP   IDENTIFICATION IN THE EXCISION COMPLEX, AND SUBUNIT.
RX   PubMed=25114241; DOI=10.1073/pnas.1413019111;
RA   Seah N.E., Warren D., Tong W., Laxmikanthan G., Van Duyne G.D., Landy A.;
RT   "Nucleoprotein architectures regulating the directionality of viral
RT   integration and excision.";
RL   Proc. Natl. Acad. Sci. U.S.A. 111:12372-12377(2014).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 177-356.
RX   PubMed=9082984; DOI=10.1126/science.276.5309.126;
RA   Kwon H.J., Tirumalai R., Landy A., Ellenberger T.;
RT   "Flexibility in DNA recombination: structure of the lambda integrase
RT   catalytic core.";
RL   Science 276:126-131(1997).
RN   [8]
RP   STRUCTURE BY NMR OF 1-64.
RX   PubMed=11904406; DOI=10.1073/pnas.052017999;
RA   Wojciak J.M., Sarkar D., Landy A., Clubb R.T.;
RT   "Arm-site binding by lambda-integrase: solution structure and functional
RT   characterization of its amino-terminal domain.";
RL   Proc. Natl. Acad. Sci. U.S.A. 99:3434-3439(2002).
RN   [9]
RP   X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF 74-356 IN COMPLEX WITH
RP   PHOSPHOTYROSINE.
RX   PubMed=12887904; DOI=10.1016/s1097-2765(03)00268-5;
RA   Aihara H., Kwon H.J., Nunes-Duby S.E., Landy A., Ellenberger T.;
RT   "A conformational switch controls the DNA cleavage activity of lambda
RT   integrase.";
RL   Mol. Cell 12:187-198(2003).
RN   [10]
RP   X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) OF 74-356 IN COMPLEX WITH
RP   PHOSPHOTYROSINE, AND ACTIVE SITE.
RX   PubMed=15973401; DOI=10.1038/nature03657;
RA   Biswas T., Aihara H., Radman-Livaja M., Filman D., Landy A.,
RA   Ellenberger T.;
RT   "A structural basis for allosteric control of DNA recombination by lambda
RT   integrase.";
RL   Nature 435:1059-1066(2005).
RN   [11]
RP   X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 75-176.
RX   PubMed=18540053; DOI=10.1107/s174430910801381x;
RA   Kamadurai H.B., Jain R., Foster M.P.;
RT   "Crystallization and structure determination of the core-binding domain of
RT   bacteriophage lambda integrase.";
RL   Acta Crystallogr. F 64:470-473(2008).
RN   [12]
RP   STRUCTURE BY NMR OF 1-64.
RX   PubMed=19324050; DOI=10.1016/j.jmb.2009.03.041;
RA   Fadeev E.A., Sam M.D., Clubb R.T.;
RT   "NMR structure of the amino-terminal domain of the lambda integrase protein
RT   in complex with DNA: immobilization of a flexible tail facilitates beta-
RT   sheet recognition of the major groove.";
RL   J. Mol. Biol. 388:682-690(2009).
CC   -!- FUNCTION: Integrase is necessary for integration of the phage into the
CC       host genome by site-specific recombination. In conjunction with
CC       excisionase, integrase is also necessary for excision of the prophage
CC       from the host genome. {ECO:0000269|PubMed:15973401,
CC       ECO:0000303|PubMed:16139195}.
CC   -!- SUBUNIT: Homotetramer. Interacts (via N-terminus) with the excisionase
CC       (via C-terminus) (PubMed:12832614). Part of the excision complex made
CC       of the integrase tetramer, IHF, Fis and Xis.
CC       {ECO:0000269|PubMed:12832614, ECO:0000269|PubMed:25114241}.
CC   -!- SIMILARITY: Belongs to the 'phage' integrase family. {ECO:0000305}.
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DR   EMBL; J02459; AAA96562.1; -; Genomic_DNA.
DR   PIR; A04322; RSBPIL.
DR   RefSeq; NP_040609.1; NC_001416.1.
DR   PDB; 1AE9; X-ray; 1.90 A; A/B=177-355.
DR   PDB; 1KJK; NMR; -; A=1-64.
DR   PDB; 1P7D; X-ray; 2.95 A; A/B=74-356.
DR   PDB; 1Z19; X-ray; 2.80 A; A/B=74-356.
DR   PDB; 1Z1B; X-ray; 3.80 A; A/B=1-356.
DR   PDB; 1Z1G; X-ray; 4.40 A; A/B/C/D=1-356.
DR   PDB; 2OXO; X-ray; 2.00 A; A=75-176.
DR   PDB; 2WCC; NMR; -; 3=1-64.
DR   PDB; 5J0N; EM; 11.00 A; E/F/G/H=1-356.
DR   PDBsum; 1AE9; -.
DR   PDBsum; 1KJK; -.
DR   PDBsum; 1P7D; -.
DR   PDBsum; 1Z19; -.
DR   PDBsum; 1Z1B; -.
DR   PDBsum; 1Z1G; -.
DR   PDBsum; 2OXO; -.
DR   PDBsum; 2WCC; -.
DR   PDBsum; 5J0N; -.
DR   SMR; P03700; -.
DR   DIP; DIP-41000N; -.
DR   IntAct; P03700; 10.
DR   PRIDE; P03700; -.
DR   GeneID; 2703464; -.
DR   KEGG; vg:2703470; -.
DR   EvolutionaryTrace; P03700; -.
DR   Proteomes; UP000001711; Genome.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR   GO; GO:0008907; F:integrase activity; IEA:InterPro.
DR   GO; GO:0016740; F:transferase activity; IEA:UniProtKB-KW.
DR   GO; GO:0015074; P:DNA integration; IDA:CACAO.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0075713; P:establishment of integrated proviral latency; IEA:UniProtKB-KW.
DR   GO; GO:0032359; P:provirus excision; IEA:UniProtKB-KW.
DR   GO; GO:0046718; P:viral entry into host cell; IEA:UniProtKB-KW.
DR   GO; GO:0044826; P:viral genome integration into host DNA; IEA:UniProtKB-KW.
DR   Gene3D; 1.10.150.130; -; 1.
DR   Gene3D; 1.10.443.10; -; 1.
DR   InterPro; IPR044068; CB.
DR   InterPro; IPR016177; DNA-bd_dom_sf.
DR   InterPro; IPR011010; DNA_brk_join_enz.
DR   InterPro; IPR013762; Integrase-like_cat_sf.
DR   InterPro; IPR002104; Integrase_catalytic.
DR   InterPro; IPR015094; Integrase_lambda-typ_DNA-bd_N.
DR   InterPro; IPR010998; Integrase_recombinase_N.
DR   InterPro; IPR004107; Integrase_SAM-like_N.
DR   Pfam; PF09003; Arm-DNA-bind_1; 1.
DR   Pfam; PF02899; Phage_int_SAM_1; 1.
DR   Pfam; PF00589; Phage_integrase; 1.
DR   SUPFAM; SSF54171; SSF54171; 1.
DR   SUPFAM; SSF56349; SSF56349; 1.
DR   PROSITE; PS51900; CB; 1.
DR   PROSITE; PS51898; TYR_RECOMBINASE; 1.
PE   1: Evidence at protein level;
KW   3D-structure; DNA integration; DNA recombination; DNA-binding; Hydrolase;
KW   Reference proteome; Transferase; Viral genome excision;
KW   Viral genome integration; Virus entry into host cell.
FT   CHAIN           1..356
FT                   /note="Integrase"
FT                   /id="PRO_0000197527"
FT   DOMAIN          74..155
FT                   /note="Core-binding (CB)"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01248"
FT   DOMAIN          175..355
FT                   /note="Tyr recombinase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT   ACT_SITE        212
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT   ACT_SITE        235
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT   ACT_SITE        308
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT   ACT_SITE        311
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT   ACT_SITE        333
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01246"
FT   ACT_SITE        342
FT                   /note="O-(3'-phospho-DNA)-tyrosine intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01246,
FT                   ECO:0007744|PDB:1P7D, ECO:0007744|PDB:1Z19,
FT                   ECO:0007744|PDB:1Z1B"
FT   MUTAGEN         47
FT                   /note="E->A: Complete loss of interaction with the
FT                   integrase."
FT                   /evidence="ECO:0000269|PubMed:12832614"
FT   CONFLICT        118
FT                   /note="D -> V (in Ref. 3)"
FT                   /evidence="ECO:0000305"
FT   HELIX           9..11
FT                   /evidence="ECO:0007829|PDB:2WCC"
FT   STRAND          16..18
FT                   /evidence="ECO:0007829|PDB:1KJK"
FT   STRAND          24..27
FT                   /evidence="ECO:0007829|PDB:1KJK"
FT   TURN            29..31
FT                   /evidence="ECO:0007829|PDB:1KJK"
FT   STRAND          34..39
FT                   /evidence="ECO:0007829|PDB:1KJK"
FT   HELIX           41..57
FT                   /evidence="ECO:0007829|PDB:1KJK"
FT   HELIX           76..90
FT                   /evidence="ECO:0007829|PDB:2OXO"
FT   HELIX           94..110
FT                   /evidence="ECO:0007829|PDB:2OXO"
FT   HELIX           116..118
FT                   /evidence="ECO:0007829|PDB:2OXO"
FT   HELIX           121..133
FT                   /evidence="ECO:0007829|PDB:2OXO"
FT   HELIX           137..156
FT                   /evidence="ECO:0007829|PDB:2OXO"
FT   TURN            164..167
FT                   /evidence="ECO:0007829|PDB:1Z19"
FT   HELIX           182..191
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   HELIX           192..194
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   HELIX           198..209
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   HELIX           213..218
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   HELIX           221..223
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   STRAND          228..232
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   TURN            234..236
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   STRAND          239..243
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   TURN            249..252
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   HELIX           255..265
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   STRAND          269..272
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   HELIX           282..296
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   STRAND          301..303
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   HELIX           309..321
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   HELIX           324..331
FT                   /evidence="ECO:0007829|PDB:1AE9"
FT   STRAND          334..336
FT                   /evidence="ECO:0007829|PDB:1Z19"
FT   HELIX           339..342
FT                   /evidence="ECO:0007829|PDB:1Z19"
FT   STRAND          349..352
FT                   /evidence="ECO:0007829|PDB:1AE9"
SQ   SEQUENCE   356 AA;  40304 MW;  708D52B96E89209C CRC64;
     MGRRRSHERR DLPPNLYIRN NGYYCYRDPR TGKEFGLGRD RRIAITEAIQ ANIELFSGHK
     HKPLTARINS DNSVTLHSWL DRYEKILASR GIKQKTLINY MSKIKAIRRG LPDAPLEDIT
     TKEIAAMLNG YIDEGKAASA KLIRSTLSDA FREAIAEGHI TTNHVAATRA AKSEVRRSRL
     TADEYLKIYQ AAESSPCWLR LAMELAVVTG QRVGDLCEMK WSDIVDGYLY VEQSKTGVKI
     AIPTALHIDA LGISMKETLD KCKEILGGET IIASTRREPL SSGTVSRYFM RARKASGLSF
     EGDPPTFHEL RSLSARLYEK QISDKFAQHL LGHKSDTMAS QYRDDRGREW DKIEIK
 
 
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