DNA ligase - Bacillus halodurans

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Reviewed, UniProtKB/Swiss-Prot Q9KF37 (DNLJ_BACHD)

Last modified November 3, 2009. Version 60. History...

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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 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:	BH0649

Organism

Bacillus halodurans [Complete proteome] [HAMAP]

Taxonomic identifier

86665 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

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Protein attributes

Sequence length	669 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.
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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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 – 669

669

DNA ligase HAMAP MF_01588

PRO_0000161736

Regions

Domain

591 – 669

BRCT

Nucleotide binding

34 – 38

NAD By similarity

Nucleotide binding

83 – 84

NAD By similarity

Sites

Active site

115

N6-AMP-lysine intermediate By similarity

Metal binding

404

Zinc By similarity

Metal binding

407

Zinc By similarity

Metal binding

422

Zinc By similarity

Metal binding

427

Zinc By similarity

Binding site

113

NAD By similarity

Binding site

136

NAD By similarity

Binding site

170

NAD By similarity

Binding site

286

NAD By similarity

Binding site

310

NAD By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q9KF37-1 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: FF9784A53EE551F0
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FASTA

669

74,242

        10         20         30         40         50         60 
MERNDAERKI EKLRNQLEEY GYHYYVLDKP LVSDAEYDGL MNELIELEEA FPELKSDTSP 

        70         80         90        100        110        120 
SVRVGGPPLP HFEKVEHRTP MLSLGNAFSD QDLRDFDRRV RQVVGDEVTY SCELKIDGLA 

       130        140        150        160        170        180 
ISLIYESGRF VRGATRGDGT TGEDITQNLR TIPSIPLRLK EAVSLEVRGE AFMPKRSFEA 

       190        200        210        220        230        240 
LNEAKEAAGE ERFANPRNAA AGSLRQLDPK LAAKRHLDAF IYAIGSVEGK ELHSHHEGLN 

       250        260        270        280        290        300 
YLKTIGFKIN PESAYCESID EVIDYVNSWL ERRADLPYEI DGIVIKVDNV NFQEQLGYTA 

       310        320        330        340        350        360 
KSPRWAIAYK FPAEEVITTL LDITLNVGRT GVVTPTAELK PVTVAGTTVK RASLHNEDLI 

       370        380        390        400        410        420 
REKDIRLGDS VVVKKAGDII PEVVNVLTEL RTGEERPFSM PTHCPECGSE LVRLEGEVAL 

       430        440        450        460        470        480 
RCINPQCPAQ IREGLIHFVS RQAMNIDGLG EKVITQLFEH GLIHNVADLY KLNKDELLQL 

       490        500        510        520        530        540 
ERMGEKSVNN LLASIETSKK SSLERLLFGL GIRFVGSKAA KTLAMHFPTM TELRRASYDE 

       550        560        570        580        590        600 
LIAVNEIGEK MAASIVSYFE KPEVNELIDE LASLGVNMTY NGPKPIGEEE IADSPFAGKT 

       610        620        630        640        650        660 
VVLTGKLQAL TRGEAKEKIE ALGGKVTGSV SKNTDLLVAG EDAGSKLTKA KELNIEIWDE 


EALVKAISH

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References

[1]

"Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis."
Takami H., Nakasone K., Takaki Y., Maeno G., Sasaki R., Masui N., Fuji F., Hirama C., Nakamura Y., Ogasawara N., Kuhara S., Horikoshi K.
Nucleic Acids Res. 28:4317-4331(2000) [PubMed: 11058132] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC BAA-125 / C-125 / DSM 18197 / FERM 7344 / JCM 9153.

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Cross-references

Sequence databases
	BA000004 Genomic DNA. Translation: BAB04368.1.
PIR	A83731.
RefSeq	NP_241515.1.
3D structure databases
HSSP	HSSP built from PDB template 1B04 based on UniProtKB O87703.
ModBase	Search...
Genome annotation databases
GeneID	893092.
GenomeReviews	Gene locus BH0649 in contig BA000004_GR.
KEGG	bha:BH0649.
NMPDR	fig\|272558.1.peg.649.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q9KF37.
OMA	YKFPAQE.
Enzyme and pathway databases
BioCyc	BHAL272558:BH0649-MON.
BRENDA	6.5.1.2. 191865.
Family and domain databases
HAMAP	MF_01588. [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. 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.
ProDom	PD003944. DNAligase. 1 hit. [Graphical view] [Entries sharing at least one domain]
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_BACHD

Accession

Primary (citable) accession number: Q9KF37

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 14, 2001
Last sequence update:	October 1, 2000
Last modified:	November 3, 2009
This is version 60 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