DNA ligase - Buchnera aphidicola subsp. Baizongia pistaciae

Names and origin

Protein names

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

Gene names

Name:	ligA
Synonyms:	lig
Ordered Locus Names:	bbp_062

Organism

Buchnera aphidicola subsp. Baizongia pistaciae [Complete proteome] [HAMAP]

Taxonomic identifier

135842 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Buchnera

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Protein attributes

Sequence length	672 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 – 672

672

DNA ligase HAMAP MF_01588

PRO_0000161741

Regions

Domain

592 – 672

81

BRCT

Nucleotide binding

32 – 36

5

NAD By similarity

Nucleotide binding

82 – 83

2

NAD By similarity

Sites

Active site

115

1

N6-AMP-lysine intermediate By similarity

Metal binding

408

1

Zinc By similarity

Metal binding

411

1

Zinc By similarity

Metal binding

427

1

Zinc By similarity

Metal binding

433

1

Zinc By similarity

Binding site

113

1

NAD By similarity

Binding site

136

1

NAD By similarity

Binding site

173

1

NAD By similarity

Binding site

290

1

NAD By similarity

Binding site

314

1

NAD By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q89B02-1 [UniParc].

Last modified June 16, 2003. Version 1.
Checksum: 054B84E4D3BA6F93
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FASTA

672

76,903

        10         20         30         40         50         60 
MKDIKNYILK LQDEIRYHAY LYHTLNSPKI SDEKYDFLVI ELQRLEKKCK YSVRFKDSPT 

        70         80         90        100        110        120 
QSVGSENLPE FKKFSHITPM LSLNNVFIKN DFLKFYKKIV NNITVEKIFF CSELKFDGVA 

       130        140        150        160        170        180 
INLIYINGLL FRAVTRGNGY EGEDVTSNVN MISSVPKKLI GIDIPETLEV RGEIFMLKSD 

       190        200        210        220        230        240 
FKKLNVRLTK FKKKLFSNSR NAASGSLRHK NAKVTELRSL TFYCYGCGYC SYENFTDSHF 

       250        260        270        280        290        300 
LRLKKLKSWG FPISDYNFLH SSYDEILRFY NFIQNERYFL NFNIDGIVIK VDSICLQKSL 

       310        320        330        340        350        360 
STTSKAPRWA VAYKFSDKIK ITTIMNILYQ VGRTGVITPV AQVTPIYISG VLIKKVSLHN 

       370        380        390        400        410        420 
FNEIRRLNLN IGDSVFIKRS GDVIPHIIEV ASKCKLQRNE DISIPKFCPE CGSKLKVDSF 

       430        440        450        460        470        480 
SNIKIRCMAG LKCLSQFKKL LHYFCSKKGL NILGLGPKII DKLVDLGYVS DLSDIFDLNV 

       490        500        510        520        530        540 
SLLTKVENIG IIKSQNIIRS INNSKNVSFS KFLCSLGIFE VGSIVARSIS NYFFTLDKFM 

       550        560        570        580        590        600 
NSSKEEFLLI NGIGVNIADN LYNFINDEFN KNIIFKLSKK LNISSDINAI IDNNNTLFRK 

       610        620        630        640        650        660 
KIVFSGSFSN FSRSKIIELS KKLGIIVVSS VSKSVDYIII GKKPGRKLIK AKKFSIPGIY 

       670 
EKEFLNIINV YL

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References

[1]

"Reductive genome evolution in Buchnera aphidicola."
van Ham R.C.H.J., Kamerbeek J., Palacios C., Rausell C., Abascal F., Bastolla U., Fernandez J.M., Jimenez L., Postigo M., Silva F.J., Tamames J., Viguera E., Latorre A., Valencia A., Moran F., Moya A.
Proc. Natl. Acad. Sci. U.S.A. 100:581-586(2003) [PubMed: 12522265] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

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Cross-references

Sequence databases
EMBL GenBank DDBJ	AE016826 Genomic DNA. Translation: AAO26801.1.
RefSeq	NP_777696.1.
3D structure databases
SMR	Q89B02. Positions 1-580, 595-669.
ModBase	Search...
Genome annotation databases
GeneID	1058542.
GenomeReviews	Gene locus bbp_062 in contig AE016826_GR.
KEGG	bab:bbp062.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG620317.
OMA	PRWARAY.
Enzyme and pathway databases
BioCyc	BAPH224915:BBP_062-MONOMER.
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. [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. [Graphical view]
PIRSF	PIRSF001604. LigA. 1 hit.
SMART	SM00292. BRCT. 1 hit. SM00278. HhH1. 2 hits. SM00532. LIGANc. 1 hit. [Graphical view]
TIGRFAMs	TIGR00575. dnlj. 1 hit.
PROSITE	PS50172. BRCT. False negative. 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_BUCBP

Accession

Primary (citable) accession number: Q89B02

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 16, 2003
Last sequence update:	June 16, 2003
Last modified:	February 9, 2010
This is version 55 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