DNA ligase - Bradyrhizobium sp. (strain ORS278)

Preferred order of sections

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:	BRADO5649

Organism

Bradyrhizobium sp. (strain ORS278) [Complete proteome] [HAMAP]

Taxonomic identifier

114615 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium

Protein attributes

Sequence length	716 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

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.

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 ligase (NAD+) activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 716

716

DNA ligase HAMAP MF_01588

PRO_0000313151

Regions

Domain

638 – 716

79

BRCT

Nucleotide binding

49 – 53

5

NAD By similarity

Nucleotide binding

98 – 99

2

NAD By similarity

Sites

Active site

134

1

N6-AMP-lysine intermediate By similarity

Metal binding

437

1

Zinc By similarity

Metal binding

439

1

Zinc By similarity

Metal binding

461

1

Zinc By similarity

Metal binding

467

1

Zinc By similarity

Binding site

132

1

NAD By similarity

Binding site

155

1

NAD By similarity

Binding site

192

1

NAD By similarity

Binding site

308

1

NAD By similarity

Binding site

332

1

NAD By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

A4YZJ3 [UniParc].

Last modified May 29, 2007. Version 1.
Checksum: 6FF31B580BF4E0B7
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FASTA

716

79,735

        10         20         30         40         50         60 
MAKTAKSKQS VDVADLTKAQ AKVEWKRLAL ELETHDRLYY QEDAPKISDA AYDELRRRFN 

        70         80         90        100        110        120 
AIEKRFPELV SRDSPSQTVG AAPSGRFKKV RHAVPMLSLD NAFAEEDVRD FVGRIARFLK 

       130        140        150        160        170        180 
LAEDDRIAFS AEPKIDGLSM SLRYEGGQLV TAATRGDGAE GEDVTANIRT LKDVPQKLHG 

       190        200        210        220        230        240 
RNLPDICEIR GEVYMTKQAF LALNERQKEA GDTIFANPRN SAAGSLRQKD PTITASRPLG 

       250        260        270        280        290        300 
FFAYAWGDMS AMPAETQSGM IKWFEHCGFT TNPLTKLCHS VEELIAFHRA IEEQRAELDY 

       310        320        330        340        350        360 
DIDGVVYKVD RIDWQERLGF VSRTPRWGIA HKFPAERAMT VLKDIEIQVG RTGSFTPVGK 

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

       430        440        450        460        470        480 
IDKRPADAEV FAFPRKCPCP LHTDVVREET AAGEEGSRAR CTGEFACPYQ KIEHLKLFAS 

       490        500        510        520        530        540 
RRAFDIDGLG EKQIQFFFDE GWVKEPADIF TLQKRNAKLK LEEVEGYGET SVRNLFNAIE 

       550        560        570        580        590        600 
ARREMALERF IYALGMRYVG ETTALALARG YGSWEAFHDA CLKVANGDEE AIAEMDALDQ 

       610        620        630        640        650        660 
IGETVIKSVA AYFGEDHNRG IVERLTREVK ILDAEKPKRN SPIATKTVVF TGTLEKMTRD 

       670        680        690        700        710 
EAKATAERLG AKVSGSVSKK TDYVVAGPGA GSKLKDAEKH GVKVLTEDEW LQLIGE

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References

[1]

"Legumes symbioses: absence of nod genes in photosynthetic bradyrhizobia."
Giraud E., Moulin L., Vallenet D., Barbe V., Cytryn E., Avarre J.-C., Jaubert M., Simon D., Cartieaux F., Prin Y., Bena G., Hannibal L., Fardoux J., Kojadinovic M., Vuillet L., Lajus A., Cruveiller S., Rouy Z.

Sadowsky M.
Science 316:1307-1312(2007) [PubMed: 17540897] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ORS278.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CU234118 Genomic DNA. Translation: CAL79319.1.
RefSeq	YP_001207536.1. NC_009445.1.
3D structure databases
ProteinModelPortal	A4YZJ3.
ModBase	Search...
Protein-protein interaction databases
STRING	A4YZJ3.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	5115430.
GenomeReviews	Gene locus BRADO5649 in contig CU234118_GR.
KEGG	bra:BRADO5649.
PATRIC	21227255. VBIBraSp122330_5424.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0272.
HOGENOM	HBG620317.
OMA	ENVRTIR.
ProtClustDB	CLSK2516592.
Enzyme and pathway databases
BioCyc	BSP376:BRADO5649-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. 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.
KO	K01972.
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. SM00532. LIGANc. 1 hit. [Graphical view]
SUPFAM	SSF52113. BRCT. 1 hit. SSF50249. Nucleic_acid_OB. 1 hit. SSF47781. RuvA_2_like. 1 hit.
TIGRFAMs	TIGR00575. Dnlj. 1 hit.
PROSITE	PS50172. BRCT. 1 hit. PS01055. DNA_LIGASE_N1. 1 hit. PS01056. DNA_LIGASE_N2. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLJ_BRASO

Accession

Primary (citable) accession number: A4YZJ3

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	May 29, 2007
Last modified:	December 14, 2011
This is version 36 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

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

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents