DNA ligase - Alcanivorax borkumensis (strain SK2 / ATCC 700651 / DSM 11573)

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:	ABO_0949

Organism

Alcanivorax borkumensis (strain SK2 / ATCC 700651 / DSM 11573) [Complete proteome] [HAMAP]

Taxonomic identifier

393595 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Oceanospirillales › Alcanivoracaceae › Alcanivorax

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Protein attributes

Sequence length	777 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 – 777

777

DNA ligase HAMAP MF_01588

PRO_0000313107

Regions

Domain

691 – 777

87

BRCT

Nucleotide binding

35 – 39

5

NAD By similarity

Nucleotide binding

84 – 85

2

NAD By similarity

Sites

Active site

118

1

N6-AMP-lysine intermediate By similarity

Metal binding

411

1

Zinc By similarity

Metal binding

414

1

Zinc By similarity

Metal binding

429

1

Zinc By similarity

Metal binding

435

1

Zinc By similarity

Binding site

116

1

NAD By similarity

Binding site

139

1

NAD By similarity

Binding site

176

1

NAD By similarity

Binding site

293

1

NAD By similarity

Binding site

317

1

NAD By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q0VR01-1 [UniParc].

Last modified September 5, 2006. Version 1.
Checksum: 0A60F808E9D10703
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FASTA

777

84,628

        10         20         30         40         50         60 
MTNNNDPSLQ AQSLRDQLND WSYRYYVQDD PAVPDAEYDR VFRALKDLEA QYPDLVTADS 

        70         80         90        100        110        120 
PTQRVGDVPL DAFEQVQHEV PMLSLDNAFD DEELWAFDKR IRERLDVSEI IDYVAEPKLD 

       130        140        150        160        170        180 
GLAVSLLYEN GELVRAATRG DGQTGENITV NARTIRSVPL KLRGNDVPKR LEVRGEVVMP 

       190        200        210        220        230        240 
HAGFEELNAR QQEAGLKLFA NPRNAAAGSL RQLDSRITAS RPLEFYAYSM AQLEGWEHPP 

       250        260        270        280        290        300 
THSAMLDALR DWGLRVNPEI RVCHGVEALL RFYQGILEKR EHLDYDIDGV VYKVNRFDWQ 

       310        320        330        340        350        360 
DDLGFVSRAP RWAIAHKFPA QEELTVLNGV DWQVGRTGAL TPVARLEPVH VGGVIVSNAT 

       370        380        390        400        410        420 
LHNIDEIQRL DIRIGDTVVV YRAGDVIPKV VRALPERRPA NAQGIALPSS CPVCGSEILR 

       430        440        450        460        470        480 
GHDQVVARCT GGLICGDQRR EAIKHFASRR AMDIDGLGDK LVDALVDQEL ITTVADLYRL 

       490        500        510        520        530        540 
KAEQVAGLER MGEKSADNLI AALEASKTVG LGRFLFALGI LQIGEETAKN LADCFGDLDS 

       550        560        570        580        590        600 
IRHAPLLLLL AVPDVGLEVA KAIGAFFAES DNEAVIDGLL AQGVSPQASG VPSAAFVKSL 

       610        620        630        640        650        660 
TLAQLLKSAK RLGMNLEGIG DKSLDILGSH FRTVTELSAA AAEGAGAEPK GVRSGVMTQL 

       670        680        690        700        710        720 
AKALAENDWR GRLQDAEKKV ADMAARAPQE MESQPLEGQT WVLTGTLEQF TRNQAKQALQ 

       730        740        750        760        770 
QLGAKVAGSV SKNTRMVVAG ASAGSKLAKA ESLGIEVCDE AALLSLLNQH GIDPGAL

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References

[1]

"Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis."
Schneiker S., Martins dos Santos V.A.P., Bartels D., Bekel T., Brecht M., Buhrmester J., Chernikova T.N., Denaro R., Ferrer M., Gertler C., Goesmann A., Golyshina O.V., Kaminski F., Khachane A.N., Lang S., Linke B., McHardy A.C., Meyer F.

Golyshin P.N.
Nat. Biotechnol. 24:997-1004(2006) [PubMed: 16878126] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

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Cross-references

Sequence databases
EMBL GenBank DDBJ	AM286690 Genomic DNA. Translation: CAL16397.1.
RefSeq	YP_692669.1.
3D structure databases
SMR	Q0VR01. Positions 9-588, 690-770.
ModBase	Search...
Protein-protein interaction databases
STRING	Q0VR01.
Genome annotation databases
GeneID	4211547.
GenomeReviews	Gene locus ABO_0949 in contig AM286690_GR.
KEGG	abo:ABO_0949.
NMPDR	fig\|393595.12.peg.949.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0272.
HOGENOM	HBG620317.
OMA	IKHFASR.
PhylomeDB	Q0VR01.
Enzyme and pathway databases
BioCyc	ABOR393595:ABO_0949-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. 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]
PIRSF	PIRSF001604. LigA. 1 hit.
SMART	SM00292. BRCT. 1 hit. SM00278. HhH1. 3 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_ALCBS

Accession

Primary (citable) accession number: Q0VR01

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	September 5, 2006
Last modified:	February 9, 2010
This is version 33 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

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents