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Reviewed, UniProtKB/Swiss-Prot Q89FV8 (DNLJ_BRAJA)

Last modified November 3, 2009. Version 47. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    DNA ligase
    EC=6.5.1.2
Alternative name(s):
    Polydeoxyribonucleotide synthase [NAD+]
Gene names
Name: ligA
Ordered Locus Names: bll6591
OrganismBradyrhizobium japonicum [Complete proteome] [HAMAP]
Taxonomic identifier375 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium

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Protein attributes

Sequence length716 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceInferred 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.

Catalytic activity

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + nicotinamide nucleotide + (deoxyribonucleotide)(n+m). HAMAP MF_01588

Cofactor

Magnesium or manganese By similarity.

Sequence similarities

Belongs to the NAD-dependent DNA ligase family. LigA subfamily.

Contains 1 BRCT domain.

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Ontologies

Keywords
   Biological processDNA damage
DNA repair
DNA replication
   LigandMagnesium
Manganese
Metal-binding
NAD
Zinc
   Molecular functionLigase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological processDNA repair

Inferred from electronic annotation. Source: UniProtKB-KW

DNA replication

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentintracellular

Inferred from electronic annotation. Source: InterPro

   Molecular functionDNA 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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 716716DNA ligase HAMAP MF_01588
PRO_0000313149

Regions

Domain638 – 71679BRCT
Nucleotide binding50 – 545NAD By similarity
Nucleotide binding99 – 1002NAD By similarity

Sites

Active site1341N6-AMP-lysine intermediate By similarity
Metal binding4371Zinc By similarity
Metal binding4391Zinc By similarity
Metal binding4611Zinc By similarity
Metal binding4671Zinc By similarity
Binding site1321NAD By similarity
Binding site1551NAD By similarity
Binding site1921NAD By similarity
Binding site3081NAD By similarity
Binding site3321NAD By similarity

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Sequences

Sequence LengthMass (Da)Tools
Q89FV8-1 [UniParc].

Last modified June 1, 2003. Version 1.
Checksum: E31CDDC5B2928161

FASTA71679,565
        10         20         30         40         50         60 
MMARAAKSKP LRDVAELTKA QAKVELMRLA LELEGHDKRY YQDDAPTVTD AEYDALRQRF 

        70         80         90        100        110        120 
NAIEKRFPEF VSAESPSQKV GAAPSGRFRK VRHAVPMLSL DNAFAEEDVR DFVGRIVRFL 

       130        140        150        160        170        180 
KLDDDKIDFS AEPKIDGLSM SLRYEGGELV TAATRGDGAE GEDVTANIRT LEDVPQKLKG 

       190        200        210        220        230        240 
RNVPDICEVR GEVYMTKKAF LALNERQKAA GDTIFANPRN SAAGSLRQKD PTITASRPLG 

       250        260        270        280        290        300 
FFAYAWGEMS AMPEETQTGM IHWFERCGFK TNPLTRLCHS VEELIAFHQR IEEERAELDY 

       310        320        330        340        350        360 
DIDGVVYKVD RIDWQERLGF VSRTPRWGIA HKFPAEQAMT VLRDIEIQVG RTGSFTPVGK 

       370        380        390        400        410        420 
LEPVGVGGVI VQNVTLHNED YIKGIGNKGE VLREGRDIRI GDTVVIQRAG DVIPQVVDVV 

       430        440        450        460        470        480 
LDKRPKTAKE FHFPKTCPCP LHTDVTREET AAGEEGSRAR CTGEFACPYQ KIEHLKLFVS 

       490        500        510        520        530        540 
RRAFDIDGLG EKQLQYFFDE GFVKEPADIF TLEKRNAKLK LEEIEGYGAT SVRNLFAAIE 

       550        560        570        580        590        600 
SRRRIALERF VYALGMRHVG ETTALALARG YGSWEAFHDA CLKVAKGDEE AMADMDALDQ 

       610        620        630        640        650        660 
IGDTVIKSIA DYFGESHNRG IVERLTKEVE IVDAEKPKSN SAVAGKTVVF TGSLEKMTRD 

       670        680        690        700        710 
EAKATAERLG AKVSGSVSKK TDLVVAGPGA GSKLAEANKH GVKVLTEDEW LKLIGE

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References

[1]"Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110."
Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.
DNA Res. 9:189-197(2002) [PubMed: 12597275] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: USDA 110.

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Cross-references

Sequence databases

BA000040 Genomic DNA. Translation: BAC51856.1.
RefSeqNP_773231.1.

3D structure databases

HSSPHSSP built from PDB template 1L7B based on UniProtKB P26996.
ModBaseSearch...

Genome annotation databases

GeneID1052344.
GenomeReviewsGene locus bll6591 in contig BA000040_GR.
KEGGbja:bll6591.
NMPDRfig|224911.1.peg.6591.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMQ89FV8.
OMAYKFPAQE.

Enzyme and pathway databases

BioCycBJAP224911:BLL6591-MON.
BRENDA6.5.1.2. 280.

Family and domain databases

HAMAPMF_01588.
[Tree]
InterProIPR001357. BRCT.
IPR018239. DNA_ligase_AS.
IPR004150. DNA_ligase_OB.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR012340. NA-bd_OB-fold.
[Graphical view]
Gene3DG3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
PfamPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
[Graphical view]
PIRSFPIRSF001604. LigA. 1 hit.
ProDomPD003944. DNAligase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00292. BRCT. 1 hit.
SM00532. LIGANc. 1 hit.
[Graphical view]
TIGRFAMsTIGR00575. dnlj. 1 hit.
PROSITEPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. False negative.
[Graphical view]
ProtoNetSearch...

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Entry information

Entry nameDNLJ_BRAJA
AccessionPrimary (citable) accession number: Q89FV8
Entry history
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: June 1, 2003
Last modified: November 3, 2009
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHAMAP (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) · Sequences · References · Cross-references · Entry information · Relevant documents