DNA ligase - Bifidobacterium longum

Names and origin

Protein names

Recommended name:
    DNA ligase
    EC=6.5.1.2
Alternative name(s):
    Polydeoxyribonucleotide synthase [NAD+]

Gene names

Name:	ligA
Ordered Locus Names:	BL0052

Organism

Bifidobacterium longum [Complete proteome] [HAMAP]

Taxonomic identifier

216816 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Bifidobacteriales › Bifidobacteriaceae › Bifidobacterium

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Protein attributes

Sequence length	920 AA.
Sequence status	Complete.
Protein existence	Inferred from homology.

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General annotation (Comments)

Function	DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA By similarity. HAMAP MF_01588
Catalytic activity	NAD⁺ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + nicotinamide nucleotide + (deoxyribonucleotide)(n+m). HAMAP MF_01588
Cofactor	Magnesium or manganese By similarity. HAMAP MF_01588
Sequence similarities	Belongs to the NAD-dependent DNA ligase family. LigA subfamily. Contains 1 BRCT domain.

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Ontologies

Keywords
Biological process	DNA damage DNA repair DNA replication
Ligand	Magnesium Manganese Metal-binding NAD Zinc
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (NAD+) activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 920

920

DNA ligase HAMAP MF_01588

PRO_0000313140

Regions

Domain

839 – 920

82

BRCT

Nucleotide binding

90 – 94

5

NAD By similarity

Nucleotide binding

139 – 140

2

NAD By similarity

Sites

Active site

175

1

N6-AMP-lysine intermediate By similarity

Metal binding

481

1

Zinc By similarity

Metal binding

484

1

Zinc By similarity

Metal binding

500

1

Zinc By similarity

Metal binding

506

1

Zinc By similarity

Binding site

173

1

NAD By similarity

Binding site

196

1

NAD By similarity

Binding site

235

1

NAD By similarity

Binding site

360

1

NAD By similarity

Binding site

384

1

NAD By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q8G830-1 [UniParc].

Last modified March 1, 2003. Version 1.
Checksum: 95ADA05406F38619
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FASTA

920

99,855

        10         20         30         40         50         60 
MSTNEQLAWD FDDGDVAEVR PDTGIARFAP GSEQWIAALQ PTDDDAIRLD RFDVNTMTAE 

        70         80         90        100        110        120 
AAARLWARVA AWVESDQIAY YIDDSPVSSD AAYDARMRCL ERLEAAFPSL DNPQSPTHRV 

       130        140        150        160        170        180 
GGSFSNDFAS VRHPSRMMSL DDVFSIEELK DWYDSVIRDL DWPESKPLPM SCEVKIDGLA 

       190        200        210        220        230        240 
LNLIYRNGVL EQGLTRGDGV TGEDITLNVR TIGSIPANLG GPKEDVPDFV EIRGEVFMRW 

       250        260        270        280        290        300 
DDFHTLNNEQ EDAGRAPFAN PRNAAAGSLR QKDPRITATR RLSFYAHGLG QLTWGPDHPR 

       310        320        330        340        350        360 
GTHDVVADQS QAYDLYTKWG VPVSPHNRAV TSFQEILDMI EYYGEHRGDI EHALDGIVVK 

       370        380        390        400        410        420 
VDDLGLQRTL GATSRAPRWA IAYKYPPEEV NTELLNITVQ VGRTGRVTPV AVLKPVYVAG 

       430        440        450        460        470        480 
STVARTTLHN GFEVKRKGIL IGDTVVVRKA GDVIPELVGP VLERRKGRED QLREFVMPEF 

       490        500        510        520        530        540 
CPSCGAKLSP AKEGDKDIRC PNVESCPAQL TERVISLASR KAFDIEHLGE QSAIALTNPE 

       550        560        570        580        590        600 
ENRPDSVATY APNITEVLVA PGEEPDPYEP VEGLELPAAQ KPVLSNESGL FNLTAADLRD 

       610        620        630        640        650        660 
VRVWREAAIV EVHETVGANG KKKKVRKRVG GSGLWHQVPA FWTAPTPAKK LTAKQLAERA 

       670        680        690        700        710        720 
QGEAAIESAE TQGDTASETT GAPTGAEAPL GTMPGFAAAS YPEYDVPADA VIVRVDHKTT 

       730        740        750        760        770        780 
RTGVTDVPVI IRPGENTRKM FDEMDKARHA DLWRVLVALS IRRLGPPTAR LIASAMGSLA 

       790        800        810        820        830        840 
AIENATIEDL TAIDGVGPEI AESVVNWFAA TREPGDWRGA TLRAWQAAGV GVDEAETSSL 

       850        860        870        880        890        900 
PQTLAGKTVV VTGSLEGYSR DSAKEAIIER GGKAAGSVSK KTDYVVIGAN AGSKAAKAEE 

       910        920 
LGIPMLSETQ FAQLLATGTI

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References

[1]

"The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract."
Schell M.A., Karmirantzou M., Snel B., Vilanova D., Berger B., Pessi G., Zwahlen M.-C., Desiere F., Bork P., Delley M., Pridmore R.D., Arigoni F.
Proc. Natl. Acad. Sci. U.S.A. 99:14422-14427(2002) [PubMed: 12381787] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: NCC 2705.

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Cross-references

Sequence databases
EMBL GenBank DDBJ	AE014295 Genomic DNA. Translation: AAN23919.1.
RefSeq	NP_695283.1.
3D structure databases
HSSP	HSSP built from PDB template 1ZAU based on UniProtKB P63973.
SMR	Q8G830. Positions 67-388, 77-831, 841-918.
ModBase	Search...
Genome annotation databases
GeneID	1023212.
GenomeReviews	Gene locus BL0052 in contig AE014295_GR.
KEGG	blo:BL0052.
NMPDR	fig\|206672.1.peg.52.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG620317.
OMA	IKHFASR.
Enzyme and pathway databases
BioCyc	BLON206672:BL0052-MONOMER.
BRENDA	6.5.1.2. 39917.
Family and domain databases
HAMAP	MF_01588. DNA_ligase_A. [Tree]
InterPro	IPR001357. BRCT. IPR018239. DNA_ligase_AS. IPR004150. DNA_ligase_OB. IPR001679. DNAligase. IPR013839. DNAligase_adenylation. IPR013840. DNAligase_N. IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif. IPR012340. NA-bd_OB-fold. IPR016027. NA-bd_OB-fold-like. IPR010994. RuvA_2-like. IPR004149. Znf_DNAligase_C4. [Graphical view]
Gene3D	G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
Pfam	PF00533. BRCT. 1 hit. PF01653. DNA_ligase_aden. 1 hit. PF03120. DNA_ligase_OB. 1 hit. PF03119. DNA_ligase_ZBD. 1 hit. [Graphical view]
SMART	SM00292. BRCT. 1 hit. SM00278. HhH1. 2 hits. SM00532. LIGANc. 1 hit. [Graphical view]
TIGRFAMs	TIGR00575. dnlj. 1 hit.
PROSITE	PS50172. BRCT. 1 hit. PS01055. DNA_LIGASE_N1. 1 hit. PS01056. DNA_LIGASE_N2. 1 hit. [Graphical view]
ProtoNet	Search...

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Entry information

Entry name

DNLJ_BIFLO

Accession

Primary (citable) accession number: Q8G830

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	March 1, 2003
Last modified:	February 9, 2010
This is version 50 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents