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Database: UniProt/SWISS-PROT
Entry: DNLI_PYRFU
LinkDB: DNLI_PYRFU
Original site: DNLI_PYRFU 
ID   DNLI_PYRFU              Reviewed;         561 AA.
AC   P56709;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   30-MAY-2000, sequence version 1.
DT   28-MAR-2018, entry version 120.
DE   RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_00407};
DE            EC=6.5.1.1 {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000269|PubMed:16820169};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] {ECO:0000255|HAMAP-Rule:MF_00407};
GN   Name=lig {ECO:0000255|HAMAP-Rule:MF_00407}; OrderedLocusNames=PF1635;
OS   Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Pyrococcus.
OX   NCBI_TaxID=186497;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF N-TERMINUS.
RC   STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RA   Mathur E.J., Marsh E.J., Schoettlin W.E.;
RT   "Purified thermostable Pyrococcus furiosus DNA ligase.";
RL   Patent number US5700672, 23-DEC-1997.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX   PubMed=10430560;
RA   Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA   DiRuggiero J., Robb F.T.;
RT   "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and
RT   P. horikoshii inferred from complete genomic sequences.";
RL   Genetics 152:1299-1305(1999).
RN   [3]
RP   X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANT ALA-534 IN COMPLEX
RP   WITH AMP, ACTIVE SITE, CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS
RP   OF LYS-249; ARG-531 AND LYS-534.
RX   PubMed=16820169; DOI=10.1016/j.jmb.2006.05.062;
RA   Nishida H., Kiyonari S., Ishino Y., Morikawa K.;
RT   "The closed structure of an archaeal DNA ligase from Pyrococcus
RT   furiosus.";
RL   J. Mol. Biol. 360:956-967(2006).
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA
CC       during DNA replication, DNA recombination and DNA repair.
CC       {ECO:0000255|HAMAP-Rule:MF_00407}.
CC   -!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
CC       5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
CC       AMP + diphosphate. {ECO:0000255|HAMAP-Rule:MF_00407,
CC       ECO:0000269|PubMed:16820169}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00407,
CC         ECO:0000305|PubMed:16820169};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Temperature dependence:
CC         Optimum temperature is about 70 degrees Celsius. Active from 4
CC         to 100 degrees Celsius. Thermostable.;
CC   -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:16820169}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00407}.
DR   EMBL; AE009950; AAL81759.1; -; Genomic_DNA.
DR   RefSeq; WP_011012782.1; NC_003413.1.
DR   PDB; 2CFM; X-ray; 1.80 A; A=1-561.
DR   PDBsum; 2CFM; -.
DR   ProteinModelPortal; P56709; -.
DR   SMR; P56709; -.
DR   DIP; DIP-48778N; -.
DR   IntAct; P56709; 1.
DR   STRING; 186497.PF1635; -.
DR   PRIDE; P56709; -.
DR   EnsemblBacteria; AAL81759; AAL81759; PF1635.
DR   GeneID; 1469512; -.
DR   KEGG; pfu:PF1635; -.
DR   PATRIC; fig|186497.12.peg.1701; -.
DR   eggNOG; arCOG01347; Archaea.
DR   eggNOG; COG1793; LUCA.
DR   HOGENOM; HOG000036008; -.
DR   KO; K10747; -.
DR   OMA; WLFEESY; -.
DR   OrthoDB; POG093Z03L0; -.
DR   BRENDA; 6.5.1.1; 5243.
DR   EvolutionaryTrace; P56709; -.
DR   Proteomes; UP000001013; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR   GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR   GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro.
DR   GO; GO:0051103; P:DNA ligation involved in DNA repair; IEA:InterPro.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR   Gene3D; 1.10.3260.10; -; 1.
DR   HAMAP; MF_00407; DNA_ligase; 1.
DR   InterPro; IPR022865; DNA_ligae_ATP-dep_bac/arc.
DR   InterPro; IPR000977; DNA_ligase_ATP-dep.
DR   InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR   InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR   InterPro; IPR016059; DNA_ligase_ATP-dep_CS.
DR   InterPro; IPR012308; DNA_ligase_ATP-dep_N.
DR   InterPro; IPR036599; DNA_ligase_N_sf.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   Pfam; PF04679; DNA_ligase_A_C; 1.
DR   Pfam; PF01068; DNA_ligase_A_M; 1.
DR   Pfam; PF04675; DNA_ligase_A_N; 1.
DR   SUPFAM; SSF117018; SSF117018; 1.
DR   SUPFAM; SSF50249; SSF50249; 1.
DR   TIGRFAMs; TIGR00574; dnl1; 1.
DR   PROSITE; PS00697; DNA_LIGASE_A1; 1.
DR   PROSITE; PS00333; DNA_LIGASE_A2; 1.
DR   PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Cell cycle; Cell division;
KW   Complete proteome; Direct protein sequencing; DNA damage;
KW   DNA recombination; DNA repair; DNA replication; Ligase; Magnesium;
KW   Metal-binding; Nucleotide-binding; Reference proteome.
FT   CHAIN         1    561       DNA ligase.
FT                                /FTId=PRO_0000059613.
FT   ACT_SITE    249    249       N6-AMP-lysine intermediate.
FT                                {ECO:0000255|HAMAP-Rule:MF_00407,
FT                                ECO:0000269|PubMed:16820169}.
FT   BINDING     247    247       ATP. {ECO:0000244|PDB:2CFM,
FT                                ECO:0000255|HAMAP-Rule:MF_00407,
FT                                ECO:0000269|PubMed:16820169}.
FT   BINDING     254    254       ATP. {ECO:0000244|PDB:2CFM,
FT                                ECO:0000255|HAMAP-Rule:MF_00407,
FT                                ECO:0000269|PubMed:16820169}.
FT   BINDING     269    269       ATP. {ECO:0000244|PDB:2CFM,
FT                                ECO:0000255|HAMAP-Rule:MF_00407,
FT                                ECO:0000269|PubMed:16820169}.
FT   BINDING     299    299       ATP. {ECO:0000244|PDB:2CFM,
FT                                ECO:0000255|HAMAP-Rule:MF_00407,
FT                                ECO:0000269|PubMed:16820169}.
FT   BINDING     339    339       ATP. {ECO:0000244|PDB:2CFM,
FT                                ECO:0000255|HAMAP-Rule:MF_00407,
FT                                ECO:0000269|PubMed:16820169}.
FT   BINDING     414    414       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     420    420       ATP. {ECO:0000244|PDB:2CFM,
FT                                ECO:0000255|HAMAP-Rule:MF_00407,
FT                                ECO:0000269|PubMed:16820169}.
FT   MUTAGEN     249    249       K->A: Loss of N6-AMP-lysine intermediate.
FT                                {ECO:0000269|PubMed:16820169}.
FT   MUTAGEN     531    531       R->A: Reduced ATP binding and enzyme
FT                                activity; when associated with A-534.
FT                                {ECO:0000269|PubMed:16820169}.
FT   MUTAGEN     534    534       K->A: Reduced ATP binding and enzyme
FT                                activity; when associated with A-531.
FT                                {ECO:0000269|PubMed:16820169}.
FT   HELIX         3     14       {ECO:0000244|PDB:2CFM}.
FT   HELIX        19     32       {ECO:0000244|PDB:2CFM}.
FT   HELIX        35     37       {ECO:0000244|PDB:2CFM}.
FT   TURN         38     40       {ECO:0000244|PDB:2CFM}.
FT   HELIX        41     45       {ECO:0000244|PDB:2CFM}.
FT   HELIX        62     73       {ECO:0000244|PDB:2CFM}.
FT   HELIX        77     87       {ECO:0000244|PDB:2CFM}.
FT   HELIX        90    101       {ECO:0000244|PDB:2CFM}.
FT   TURN        102    104       {ECO:0000244|PDB:2CFM}.
FT   HELIX       113    125       {ECO:0000244|PDB:2CFM}.
FT   STRAND      128    130       {ECO:0000244|PDB:2CFM}.
FT   HELIX       131    143       {ECO:0000244|PDB:2CFM}.
FT   HELIX       148    159       {ECO:0000244|PDB:2CFM}.
FT   HELIX       168    178       {ECO:0000244|PDB:2CFM}.
FT   HELIX       183    193       {ECO:0000244|PDB:2CFM}.
FT   HELIX       196    213       {ECO:0000244|PDB:2CFM}.
FT   STRAND      226    231       {ECO:0000244|PDB:2CFM}.
FT   HELIX       233    239       {ECO:0000244|PDB:2CFM}.
FT   STRAND      244    249       {ECO:0000244|PDB:2CFM}.
FT   STRAND      252    260       {ECO:0000244|PDB:2CFM}.
FT   STRAND      263    267       {ECO:0000244|PDB:2CFM}.
FT   HELIX       275    277       {ECO:0000244|PDB:2CFM}.
FT   HELIX       279    288       {ECO:0000244|PDB:2CFM}.
FT   STRAND      291    303       {ECO:0000244|PDB:2CFM}.
FT   STRAND      307    309       {ECO:0000244|PDB:2CFM}.
FT   HELIX       313    320       {ECO:0000244|PDB:2CFM}.
FT   HELIX       325    331       {ECO:0000244|PDB:2CFM}.
FT   STRAND      334    344       {ECO:0000244|PDB:2CFM}.
FT   HELIX       354    364       {ECO:0000244|PDB:2CFM}.
FT   STRAND      369    373       {ECO:0000244|PDB:2CFM}.
FT   STRAND      376    380       {ECO:0000244|PDB:2CFM}.
FT   HELIX       382    394       {ECO:0000244|PDB:2CFM}.
FT   STRAND      399    403       {ECO:0000244|PDB:2CFM}.
FT   STRAND      414    421       {ECO:0000244|PDB:2CFM}.
FT   STRAND      428    437       {ECO:0000244|PDB:2CFM}.
FT   HELIX       440    442       {ECO:0000244|PDB:2CFM}.
FT   STRAND      445    454       {ECO:0000244|PDB:2CFM}.
FT   TURN        456    458       {ECO:0000244|PDB:2CFM}.
FT   STRAND      461    467       {ECO:0000244|PDB:2CFM}.
FT   HELIX       473    483       {ECO:0000244|PDB:2CFM}.
FT   HELIX       484    486       {ECO:0000244|PDB:2CFM}.
FT   STRAND      487    491       {ECO:0000244|PDB:2CFM}.
FT   STRAND      494    497       {ECO:0000244|PDB:2CFM}.
FT   STRAND      502    506       {ECO:0000244|PDB:2CFM}.
FT   STRAND      508    511       {ECO:0000244|PDB:2CFM}.
FT   STRAND      514    516       {ECO:0000244|PDB:2CFM}.
FT   STRAND      521    524       {ECO:0000244|PDB:2CFM}.
FT   STRAND      526    530       {ECO:0000244|PDB:2CFM}.
FT   HELIX       536    538       {ECO:0000244|PDB:2CFM}.
FT   HELIX       542    557       {ECO:0000244|PDB:2CFM}.
SQ   SEQUENCE   561 AA;  63773 MW;  534158525B9D24B2 CRC64;
     MRYLELAQLY QKLEKTTMKL IKTRLVADFL KKVPDDHLEF IPYLILGEVF PEWDERELGV
     GEKLLIKAVA MATGIDAKEI EESVKDTGDL GESIALAVKK KKQKSFFSQP LTIKRVYQTL
     VKVAETTGEG SQDKKVKYLA DLFMDAEPLE AKYLARTILG TMRTGVAEGL LRDAIAMAFH
     VKVELVERAY MLTSDFGYVA KIAKLEGNEG LAKVQVQLGK PIKPMLAQQA ASIRDALLEM
     GGEAEFEIKY DGARVQVHKD GSKIIVYSRR LENVTRAIPE IVEALKEAII PEKAIVEGEL
     VAIGENGRPL PFQYVLRRFR RKHNIEEMME KIPLELNLFD VLYVDGQSLI DTKFIDRRRT
     LEEIIKQNEK IKVAENLITK KVEEAEAFYK RALEMGHEGL MAKRLDAVYE PGNRGKKWLK
     IKPTMENLDL VIIGAEWGEG RRAHLFGSFI LGAYDPETGE FLEVGKVGSG FTDDDLVEFT
     KMLKPLIIKE EGKRVWLQPK VVIEVTYQEI QKSPKYRSGF ALRFPRFVAL RDDKGPEDAD
     TIERIAQLYE LQEKMKGKVE S
//
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