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Reviewed, UniProtKB/Swiss-Prot Q5YRS7 (DNLJ2_NOCFA)

Last modified November 3, 2009. Version 40. 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 2
    EC=6.5.1.2
Alternative name(s):
    Polydeoxyribonucleotide synthase [NAD+] 2
Gene names
Name: ligA2
Ordered Locus Names: NFA_42650
OrganismNocardia farcinica [Complete proteome] [HAMAP]
Taxonomic identifier37329 [NCBI]
Taxonomic lineageBacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Nocardiaceae › Nocardia

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Protein attributes

Sequence length683 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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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 683683DNA ligase 2 HAMAP MF_01588
PRO_0000313343

Regions

Domain592 – 68190BRCT
Nucleotide binding27 – 315NAD By similarity
Nucleotide binding76 – 772NAD By similarity

Sites

Active site1081N6-AMP-lysine intermediate By similarity
Metal binding4031Zinc By similarity
Metal binding4061Zinc By similarity
Metal binding4221Zinc By similarity
Metal binding4281Zinc By similarity
Binding site1061NAD By similarity
Binding site1291NAD By similarity
Binding site1691NAD By similarity
Binding site2851NAD By similarity
Binding site3091NAD By similarity

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Sequences

Sequence LengthMass (Da)Tools
Q5YRS7-1 [UniParc].

Last modified November 23, 2004. Version 1.
Checksum: B4311C800344876F

FASTA68374,351
        10         20         30         40         50         60 
MRWQRLAEEV REHQFRYYVR DAPIISDGEF DALLRELQEL EDRHPDLRTP DSPTQLVGGG 

        70         80         90        100        110        120 
FATDFTPVDH LERMLSLDNV FDVDELRAWA ARVEAETGPD LHYLCEVKID GVALNLVYER 

       130        140        150        160        170        180 
GKLVRAATRG DGRTGEDVTL NARTIEDVPG ELSAGGEFPV PELLEVRGEV YLRLADFEAL 

       190        200        210        220        230        240 
NAAIVAEGKP PYANPRNTAA GSLRQKDPAV TARRRLRMIC HGLGRIEGYT PASQFEAYRA 

       250        260        270        280        290        300 
LSAWGLPVSE HTRRVRGIDA VIERVAYWGE HRHDIEHEID GQVIKVDETS LQRRLGATSR 

       310        320        330        340        350        360 
APRWAIAYKY PPEEATTKLR AIEVNVGRTG RVTPFAVMEP VVIAGSTVAM ATLHNASEVK 

       370        380        390        400        410        420 
RKGVLIGDTV TIRKAGDVIP EVLGPVVDAR TGAEREFVMP THCPECGTEL APEKEGDADI 

       430        440        450        460        470        480 
RCPNQRSCPA QLRERVYHVA GRSAFDIEAL GYEAAIDLLQ SGAIGDEGDL FDLDEARLLT 

       490        500        510        520        530        540 
TSLFTNKNGS LSANGKRLLE NLDAAKDRPL WRVLVGLSIR HVGPTAARAL AAEFGSMERI 

       550        560        570        580        590        600 
EQASVDELAA TDGVGPTIAA AVAEWFTVDW HRAIVAKWRA AGVRMVDERD ESIERTLEGL 

       610        620        630        640        650        660 
SIVVTGSLQG FSRDGAKEAI LARGGKAAGS VSKKTAFVVV GDAPGAKAAK AEELGVPILD 

       670        680 
EEGFVRLLAE GPAAVAAEEP ESG

« Hide

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References

[1]"The complete genomic sequence of Nocardia farcinica IFM 10152."
Ishikawa J., Yamashita A., Mikami Y., Hoshino Y., Kurita H., Hotta K., Shiba T., Hattori M.
Proc. Natl. Acad. Sci. U.S.A. 101:14925-14930(2004) [PubMed: 15466710] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: IFM 10152.

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Cross-references

Sequence databases

AP006618 Genomic DNA. Translation: BAD59114.1.
RefSeqYP_120478.2.

3D structure databases

ModBaseSearch...

Genome annotation databases

GeneID3111219.
GenomeReviewsGene locus NFA_42650 in contig AP006618_GR.
KEGGnfa:nfa42650.
NMPDRfig|247156.1.peg.4111.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMQ5YRS7.
OMAYKFPAQE.

Enzyme and pathway databases

BioCycNFAR247156:NFA42650-MON.
BRENDA6.5.1.2. 290697.

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.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR004149. Znf_DNAligase_C4.
[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.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFPIRSF001604. LigA. 1 hit.
ProDomPD003944. DNAligase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00292. BRCT. 1 hit.
SM00278. HhH1. 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. 1 hit.
[Graphical view]
ProtoNetSearch...

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Entry information

Entry nameDNLJ2_NOCFA
AccessionPrimary (citable) accession number: Q5YRS7
Entry history
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 23, 2004
Last modified: November 3, 2009
This is version 40 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