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Entry: DNLI_MYCTU I6YB16_MYCTU
LinkDB: DNLI_MYCTU I6YB16_MYCTU
Original site: DNLI_MYCTU I6YB16_MYCTU 
ID   DNLI_MYCTU              Reviewed;         507 AA.
AC   P9WNV5; L0TBG5; P95096; Q7D671;
DT   16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT   16-APR-2014, sequence version 1.
DT   25-OCT-2017, entry version 26.
DE   RecName: Full=DNA ligase B;
DE            Short=LigB;
DE            EC=6.5.1.1 {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000269|PubMed:14985346};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] {ECO:0000255|HAMAP-Rule:MF_00407};
GN   Name=ligB; OrderedLocusNames=Rv3062;
OS   Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC   Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC   Mycobacterium; Mycobacterium tuberculosis complex.
OX   NCBI_TaxID=83332;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 25618 / H37Rv;
RX   PubMed=9634230; DOI=10.1038/31159;
RA   Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
RA   Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
RA   Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
RA   Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
RA   Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
RA   Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
RA   Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
RA   Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
RT   "Deciphering the biology of Mycobacterium tuberculosis from the
RT   complete genome sequence.";
RL   Nature 393:537-544(1998).
RN   [2]
RP   FUNCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, DOMAIN,
RP   AND DISRUPTION PHENOTYPE.
RC   STRAIN=ATCC 25618 / H37Rv;
RX   PubMed=14985346; DOI=10.1074/jbc.M401841200;
RA   Gong C., Martins A., Bongiorno P., Glickman M., Shuman S.;
RT   "Biochemical and genetic analysis of the four DNA ligases of
RT   mycobacteria.";
RL   J. Biol. Chem. 279:20594-20606(2004).
RN   [3]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=ATCC 25618 / H37Rv;
RX   PubMed=21969609; DOI=10.1074/mcp.M111.011627;
RA   Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
RA   Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
RA   Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
RA   Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
RA   Dash D., Pandey A.;
RT   "Proteogenomic analysis of Mycobacterium tuberculosis by high
RT   resolution mass spectrometry.";
RL   Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
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, ECO:0000269|PubMed:14985346}.
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:14985346}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00407,
CC         ECO:0000269|PubMed:14985346};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=0.34 mM for ATP {ECO:0000269|PubMed:14985346};
CC   -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:14985346}.
CC   -!- DISRUPTION PHENOTYPE: Not essential for growth.
CC       {ECO:0000269|PubMed:14985346}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00407}.
DR   EMBL; AL123456; CCP45871.1; -; Genomic_DNA.
DR   PIR; G70649; G70649.
DR   RefSeq; NP_217578.1; NC_000962.3.
DR   RefSeq; WP_003912069.1; NZ_KK339370.1.
DR   ProteinModelPortal; P9WNV5; -.
DR   SMR; P9WNV5; -.
DR   STRING; 83332.Rv3062; -.
DR   PaxDb; P9WNV5; -.
DR   EnsemblBacteria; CCP45871; CCP45871; Rv3062.
DR   GeneID; 887553; -.
DR   KEGG; mtu:Rv3062; -.
DR   TubercuList; Rv3062; -.
DR   eggNOG; ENOG4107QIM; Bacteria.
DR   eggNOG; COG1793; LUCA.
DR   KO; K10747; -.
DR   OMA; WLFEESY; -.
DR   PhylomeDB; P9WNV5; -.
DR   SABIO-RK; P9WNV5; -.
DR   Proteomes; UP000001584; Chromosome.
DR   GO; GO:0005618; C:cell wall; IDA:MTBBASE.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
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; IDA:MTBBASE.
DR   GO; GO:0000287; F:magnesium ion binding; IDA:MTBBASE.
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:0006266; P:DNA ligation; IDA:MTBBASE.
DR   GO; GO:0051103; P:DNA ligation involved in DNA repair; IBA:GO_Central.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006273; P:lagging strand elongation; IBA:GO_Central.
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; PS50160; DNA_LIGASE_A3; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Cell cycle; Cell division; Complete proteome; DNA damage;
KW   DNA recombination; DNA repair; DNA replication; Ligase; Magnesium;
KW   Metal-binding; Nucleotide-binding; Reference proteome.
FT   CHAIN         1    507       DNA ligase B.
FT                                /FTId=PRO_0000365231.
FT   REGION        1    172       Not required for adenylyltransferase
FT                                activity, required for nick joining.
FT   ACT_SITE    211    211       N6-AMP-lysine intermediate.
FT                                {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     209    209       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     216    216       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     231    231       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     260    260       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     300    300       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     372    372       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     378    378       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
SQ   SEQUENCE   507 AA;  53737 MW;  A382F41A7B9E5741 CRC64;
     MLLHDVAITS MDVAATSSRL TKVARIAALL HRAAPDTQLV TIIVSWLSGE LPQRHIGVGW
     AALRSLPPPA PQPALTVTGV DATLSKIGTL PGKGSQAQRA ALVAELFSAA TEAEQTFLLR
     LLGGELRQGA KGGIMADAVA QAAGLPAATV QRAAMLGGDL AAAAAAGLSG AALDTFTLRV
     GRPIGPMLAQ TATSVHDALE RHGGTTIFEA KLDGARVQIH RANDQVRIYT RSLDDVTARL
     PEVVEATLAL PVRDLVADGE AIALCPDNRP QRFQVTASRF GRSVDVAAAR ATQPLSVFFF
     DILHRDGTDL LEAPTTERLA ALDALVPARH RVDRLITSDP TDAANFLDAT LAAGHEGVMA
     KAPAARYLAG RRGAGWLKVK PVHTLDLVVL AVEWGSGRRR GKLSNIHLGA RDPATGGFVM
     VGKTFKGMTD AMLDWQTTRF HEIAVGPTDG YVVQLRPEQV VEVALDGVQR SSRYPGGLAL
     RFARVVRYRA DKDPAEADTI DAVRALY
//
  All links  
Ontology (13)   
   GO (13)   
Chemical reaction (2)   
   KEGG ENZYME (1)   
   SABIO-RK-UP (1)   
Gene (4)   
   KEGG ORTHOLOGY (1)   
   KEGG GENES (1)   
   NCBI-Gene (1)   
   TUBERCULIST (1)   
Protein sequence (2)   
   RefSeq(pep) (2)   
DNA sequence (1)   
   EMBL (1)   
Protein domain (14)   
   InterPro (8)   
   Pfam (3)   
   PROSITE (3)   
Literature (3)   
   PubMed (3)   
All databases (39)   

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ID   I6YB16_MYCTU            Unreviewed;       507 AA.
AC   I6YB16;
DT   03-OCT-2012, integrated into UniProtKB/TrEMBL.
DT   03-OCT-2012, sequence version 1.
DT   25-OCT-2017, entry version 47.
DE   RecName: Full=Probable DNA ligase {ECO:0000256|HAMAP-Rule:MF_00407};
DE            EC=6.5.1.1 {ECO:0000256|HAMAP-Rule:MF_00407};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] {ECO:0000256|HAMAP-Rule:MF_00407};
GN   Name=ligB {ECO:0000313|EMBL:AIR15843.1};
GN   Synonyms=lig {ECO:0000256|HAMAP-Rule:MF_00407};
GN   ORFNames=LH57_16715 {ECO:0000313|EMBL:AIR15843.1};
OS   Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC   Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC   Mycobacterium; Mycobacterium tuberculosis complex.
OX   NCBI_TaxID=83332 {ECO:0000313|EMBL:AIR15843.1, ECO:0000313|Proteomes:UP000031768};
RN   [1] {ECO:0000313|EMBL:AIR15843.1, ECO:0000313|Proteomes:UP000031768}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 27294 / TMC 102 / H37Rv
RC   {ECO:0000313|Proteomes:UP000031768};
RA   Hazbon M.H., Riojas M.A., Damon A.M., Alalade R.O., Cantwell B.J.,
RA   Monaco A., King S., Sohrabi A.;
RT   "Phylogenetic analysis of Mycobacterial species using whole genome
RT   sequences.";
RL   Submitted (SEP-2014) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA
CC       during DNA replication, DNA recombination and DNA repair.
CC       {ECO:0000256|HAMAP-Rule:MF_00407}.
CC   -!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
CC       5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
CC       AMP + diphosphate. {ECO:0000256|HAMAP-Rule:MF_00407,
CC       ECO:0000256|RuleBase:RU000617}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000256|HAMAP-
CC         Rule:MF_00407};
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000256|HAMAP-Rule:MF_00407, ECO:0000256|RuleBase:RU004196}.
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DR   EMBL; CP009480; AIR15843.1; -; Genomic_DNA.
DR   RefSeq; NP_217578.1; NC_000962.3.
DR   RefSeq; WP_003912069.1; NZ_KK339370.1.
DR   ProteinModelPortal; I6YB16; -.
DR   SMR; I6YB16; -.
DR   PaxDb; I6YB16; -.
DR   PRIDE; I6YB16; -.
DR   EnsemblBacteria; AIR15843; AIR15843; LH57_16715.
DR   GeneID; 887553; -.
DR   KEGG; mtu:Rv3062; -.
DR   KEGG; mtv:RVBD_3062; -.
DR   PATRIC; fig|83332.111.peg.3412; -.
DR   eggNOG; ENOG4107QIM; Bacteria.
DR   eggNOG; COG1793; LUCA.
DR   KO; K10747; -.
DR   OMA; WLFEESY; -.
DR   PhylomeDB; I6YB16; -.
DR   Proteomes; UP000031768; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-UniRule.
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-UniRule.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniRule.
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; PS50160; DNA_LIGASE_A3; 1.
PE   3: Inferred from homology;
KW   ATP-binding {ECO:0000256|HAMAP-Rule:MF_00407,
KW   ECO:0000256|RuleBase:RU000617};
KW   Cell cycle {ECO:0000256|HAMAP-Rule:MF_00407};
KW   Cell division {ECO:0000256|HAMAP-Rule:MF_00407};
KW   Complete proteome {ECO:0000313|Proteomes:UP000031768};
KW   DNA damage {ECO:0000256|HAMAP-Rule:MF_00407,
KW   ECO:0000256|RuleBase:RU000617};
KW   DNA recombination {ECO:0000256|HAMAP-Rule:MF_00407,
KW   ECO:0000256|RuleBase:RU000617};
KW   DNA repair {ECO:0000256|HAMAP-Rule:MF_00407,
KW   ECO:0000256|RuleBase:RU000617};
KW   DNA replication {ECO:0000256|HAMAP-Rule:MF_00407,
KW   ECO:0000256|RuleBase:RU000617};
KW   Ligase {ECO:0000256|HAMAP-Rule:MF_00407,
KW   ECO:0000256|RuleBase:RU000617, ECO:0000313|EMBL:AIR15843.1};
KW   Magnesium {ECO:0000256|HAMAP-Rule:MF_00407};
KW   Metal-binding {ECO:0000256|HAMAP-Rule:MF_00407};
KW   Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00407,
KW   ECO:0000256|RuleBase:RU000617}.
FT   DOMAIN      288    412       DNA_LIGASE_A3. {ECO:0000259|PROSITE:
FT                                PS50160}.
FT   ACT_SITE    211    211       N6-AMP-lysine intermediate.
FT                                {ECO:0000256|HAMAP-Rule:MF_00407}.
FT   BINDING     209    209       ATP. {ECO:0000256|HAMAP-Rule:MF_00407}.
FT   BINDING     216    216       ATP. {ECO:0000256|HAMAP-Rule:MF_00407}.
FT   BINDING     231    231       ATP. {ECO:0000256|HAMAP-Rule:MF_00407}.
FT   BINDING     260    260       ATP. {ECO:0000256|HAMAP-Rule:MF_00407}.
FT   BINDING     300    300       ATP. {ECO:0000256|HAMAP-Rule:MF_00407}.
FT   BINDING     372    372       ATP. {ECO:0000256|HAMAP-Rule:MF_00407}.
FT   BINDING     378    378       ATP. {ECO:0000256|HAMAP-Rule:MF_00407}.
SQ   SEQUENCE   507 AA;  53737 MW;  A382F41A7B9E5741 CRC64;
     MLLHDVAITS MDVAATSSRL TKVARIAALL HRAAPDTQLV TIIVSWLSGE LPQRHIGVGW
     AALRSLPPPA PQPALTVTGV DATLSKIGTL PGKGSQAQRA ALVAELFSAA TEAEQTFLLR
     LLGGELRQGA KGGIMADAVA QAAGLPAATV QRAAMLGGDL AAAAAAGLSG AALDTFTLRV
     GRPIGPMLAQ TATSVHDALE RHGGTTIFEA KLDGARVQIH RANDQVRIYT RSLDDVTARL
     PEVVEATLAL PVRDLVADGE AIALCPDNRP QRFQVTASRF GRSVDVAAAR ATQPLSVFFF
     DILHRDGTDL LEAPTTERLA ALDALVPARH RVDRLITSDP TDAANFLDAT LAAGHEGVMA
     KAPAARYLAG RRGAGWLKVK PVHTLDLVVL AVEWGSGRRR GKLSNIHLGA RDPATGGFVM
     VGKTFKGMTD AMLDWQTTRF HEIAVGPTDG YVVQLRPEQV VEVALDGVQR SSRYPGGLAL
     RFARVVRYRA DKDPAEADTI DAVRALY
//
  All links  
Ontology (10)   
   GO (10)   
Chemical reaction (1)   
   KEGG ENZYME (1)   
Gene (4)   
   KEGG ORTHOLOGY (1)   
   KEGG GENES (2)   
   NCBI-Gene (1)   
Protein sequence (2)   
   RefSeq(pep) (2)   
DNA sequence (1)   
   EMBL (1)   
Protein domain (13)   
   InterPro (8)   
   Pfam (3)   
   PROSITE (2)   
All databases (31)   

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