DNA ligase - Bacillus pumilus (strain SAFR-032)

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:	BPUM_0626

Organism

Bacillus pumilus (strain SAFR-032) [Complete proteome] [HAMAP]

Taxonomic identifier

315750 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

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Protein attributes

Sequence length	668 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 – 668

668

DNA ligase HAMAP MF_01588

PRO_0000340328

Regions

Domain

590 – 668

79

BRCT

Nucleotide binding

34 – 38

5

NAD By similarity

Nucleotide binding

83 – 84

2

NAD By similarity

Sites

Active site

115

1

N6-AMP-lysine intermediate By similarity

Metal binding

404

1

Zinc By similarity

Metal binding

407

1

Zinc By similarity

Metal binding

422

1

Zinc By similarity

Metal binding

427

1

Zinc By similarity

Binding site

113

1

NAD By similarity

Binding site

136

1

NAD By similarity

Binding site

170

1

NAD By similarity

Binding site

286

1

NAD By similarity

Binding site

310

1

NAD By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

A8FAQ1-1 [UniParc].

Last modified November 13, 2007. Version 1.
Checksum: A140C45364E650CB
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FASTA

668

74,781

        10         20         30         40         50         60 
MDKEAAKRRI EELHEILNQY NYEYHTLDRP SVPDAEYDAR MRELISLEEE HPDLKAADSP 

        70         80         90        100        110        120 
SQRVGGAVLD AFQKVRHGTP MLSLGNAFNE QDLLDFDRRV RQAVGDDIAY NVELKIDGLA 

       130        140        150        160        170        180 
VSLRYENGVF VRGATRGDGT TGEDITENLK TIRSIPLKIK RPLSIEVRGE AFMPKPSFEA 

       190        200        210        220        230        240 
LNEKRLQNEE EPFANPRNAA AGSLRQLDTK IAAKRNLDIF VYSIAELDEI GVESQSEGLD 

       250        260        270        280        290        300 
LLDELGFKTN KERRTCQTIE EVIELIETLK TKRADFSYEI DGIVIKVDSL AQQEELGFTA 

       310        320        330        340        350        360 
KSPRWAVAYK FPAEEVVTKL LDIELSVGRT GVITPTAILE PVKVAGTTVQ RASLHNEDLI 

       370        380        390        400        410        420 
KEKDIRLLDQ VIVKKAGDII PEVAGVLIDQ RTGEEKPFHM PTECPECHSE LVRIEGEVAL 

       430        440        450        460        470        480 
RCINPECPAQ IREGLIHFVS RNAMNIDGLG ERVITQLFKE QLVSRVSDLY RLTKEELIQL 

       490        500        510        520        530        540 
ERMGEKSVEN LLRSIEQSKE NSLERLLFGL GIRFIGSKAA KTLALHFGDI DQLKQATKEQ 

       550        560        570        580        590        600 
LLEVDEIGEK MADAVVTYFE KEEILNLLNE LKELGVNMTY TGPKPVKVEE SDSYFAGKTI 

       610        620        630        640        650        660 
VLTGKLEEMA RNDAKAAIEA LGGKLAGSVS KKTDLVIAGE AAGSKLTKAE ELNIEIWDEV 


KMLEELKK

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References

[1]

"Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032."
Gioia J., Yerrapragada S., Qin X., Jiang H., Igboeli O.C., Muzny D., Dugan-Rocha S., Ding Y., Hawes A., Liu W., Perez L., Kovar C., Dinh H., Lee S., Nazareth L., Blyth P., Holder M., Buhay C.

Weinstock G.M.
PLoS ONE 2:E928-E928(2007) [PubMed: 17895969] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

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Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000813 Genomic DNA. Translation: ABV61318.1.
RefSeq	YP_001485878.1.
3D structure databases
SMR	A8FAQ1. Positions 1-580, 576-666.
ModBase	Search...
Protein-protein interaction databases
STRING	A8FAQ1.
Genome annotation databases
GeneID	5619874.
GenomeReviews	Gene locus BPUM_0626 in contig CP000813_GR.
KEGG	bpu:BPUM_0626.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0272.
HOGENOM	HBG620317.
OMA	IKHFASR.
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_BACP2

Accession

Primary (citable) accession number: A8FAQ1

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 10, 2008
Last sequence update:	November 13, 2007
Last modified:	February 9, 2010
This is version 21 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

Family and domain databases

Entry information

Relevant documents