DNA ligase - Bordetella parapertussis

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Reviewed, UniProtKB/Swiss-Prot Q7W0T4 (DNLJ_BORPA)

Last modified November 3, 2009. Version 44. 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
Ordered Locus Names:	BPP3353

Organism

Bordetella parapertussis [Complete proteome] [HAMAP]

Taxonomic identifier

519 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Alcaligenaceae › Bordetella

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Protein attributes

Sequence length	696 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 – 696

696

DNA ligase HAMAP MF_01588

PRO_0000313145

Regions

Domain

618 – 696

BRCT

Nucleotide binding

36 – 40

NAD By similarity

Nucleotide binding

85 – 86

NAD By similarity

Sites

Active site

125

N6-AMP-lysine intermediate By similarity

Metal binding

437

Zinc By similarity

Metal binding

440

Zinc By similarity

Metal binding

455

Zinc By similarity

Metal binding

461

Zinc By similarity

Binding site

123

NAD By similarity

Binding site

146

NAD By similarity

Binding site

181

NAD By similarity

Binding site

319

NAD By similarity

Binding site

343

NAD By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q7W0T4-1 [UniParc].

Last modified October 1, 2003. Version 1.
Checksum: 8AB412B7D5406FAC
Show »

FASTA

696

75,503

        10         20         30         40         50         60 
MAQAGPTPQQ AIARLRAEIE QHNIRYYVHD DPSVPDAEYD ALMRDLQALE AEHPELVTPD 

        70         80         90        100        110        120 
SPTQRVGAAP LAEFGSVRHA VPMLSLGNAF DEEDVRAFDK RVADTLRGAG LLGLDQQVEY 

       130        140        150        160        170        180 
FCELKLDGLA ISLCYEEGRL AQAATRGDGQ TGEDVTANIR TIKGVPLRLH GAPRVLEVRG 

       190        200        210        220        230        240 
EVLMNRAEFE RLNRTQAARG EKVFVNPRNA AAGSLRQLDP RITAQRPLRF FAYSWGEVHG 

       250        260        270        280        290        300 
LPEGMPTRFD EPAPGVRVAS TLPRDTHGGM LDWLAELGLP VNLRHNHRER GADGLLAFYE 

       310        320        330        340        350        360 
RIGKLRADLP YDIDGVVYKV DALPSQRVLG FVARAPRFAL AHKFPAEEAV TQLLGIEVQV 

       370        380        390        400        410        420 
GRTGAITPVA RLAPVFVGGV TVTNATLHNE DEIRRKDVRI GDTVIVRRAG DVIPEVVGPV 

       430        440        450        460        470        480 
LEKRPADARE FVMLTACPIC GSAIERPEGE AIARCTGGLF CAAQRKQTLL HAAGRKALDI 

       490        500        510        520        530        540 
EGLGEKLIDQ LVDADRVKSL ADIYSLTAFE LAALERMGKK SAENLVAAID QARRPALGRL 

       550        560        570        580        590        600 
LFALGIRHVG ETTARDVARH FGSMERIMDA SEEALLAVPD VGGVVAGSIR RFFAEPHNRE 

       610        620        630        640        650        660 
IVEQLTQQGV HPQAEAEPEG TSLAGKTFVL TGTMPNWTRD EATRRILAAG GKVSGSVSKK 

       670        680        690 
TAYLVTGEDA GSKLTKAQEL GVPVLDEDGL KALLGL

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References

[1]

"Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica."
Parkhill J., Sebaihia M., Preston A., Murphy L.D., Thomson N.R., Harris D.E., Holden M.T.G., Churcher C.M., Bentley S.D., Mungall K.L., Cerdeno-Tarraga A.-M., Temple L., James K.D., Harris B., Quail M.A., Achtman M., Atkin R., Baker S.

Maskell D.J.
Nat. Genet. 35:32-40(2003) [PubMed: 12910271] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 12822 / ATCC BAA-587 / NCTC 13253.

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Cross-references

Sequence databases
	BX640433 Genomic DNA. Translation: CAE38638.1.
RefSeq	NP_885519.1.
3D structure databases
HSSP	HSSP built from PDB template 1B04 based on UniProtKB O87703.
ModBase	Search...
Genome annotation databases
GeneID	1665687.
GenomeReviews	Gene locus BPP3353 in contig BX470249_GR.
KEGG	bpa:BPP3353.
NMPDR	fig\|257311.1.peg.3153.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q7W0T4.
OMA	YKFPAQE.
Enzyme and pathway databases
BioCyc	BPAR257311:BPP3353-MON.
BRENDA	6.5.1.2. 263123.
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. IPR000445. HhH_motif. 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. PF00633. HHH. 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. 4 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_BORPA

Accession

Primary (citable) accession number: Q7W0T4

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	October 1, 2003
Last modified:	November 3, 2009
This is version 44 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