DNA ligase - Bordetella pertussis

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:	BP3560

Organism

Bordetella pertussis

Taxonomic identifier

520 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Alcaligenaceae › Bordetella

Protein attributes

Sequence length	696 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 Reference 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: 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 – 696

696

DNA ligase HAMAP MF_01588

PRO_0000313146

Regions

Domain

618 – 696

79

BRCT

Nucleotide binding

36 – 40

5

NAD By similarity

Nucleotide binding

85 – 86

2

NAD By similarity

Sites

Active site

125

1

N6-AMP-lysine intermediate By similarity

Metal binding

437

1

Zinc By similarity

Metal binding

440

1

Zinc By similarity

Metal binding

455

1

Zinc By similarity

Metal binding

461

1

Zinc By similarity

Binding site

123

1

NAD By similarity

Binding site

146

1

NAD By similarity

Binding site

181

1

NAD By similarity

Binding site

319

1

NAD By similarity

Binding site

343

1

NAD By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q7VRX7 [UniParc].

Last modified October 1, 2003. Version 1.
Checksum: 2FB4177471837EA3
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FASTA

696

75,586

        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 ISLRYEEGRL 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 GSAIERPESE 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: Tohama I / ATCC BAA-589 / NCTC 13251.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BX640421 Genomic DNA. Translation: CAE43819.1.
RefSeq	NP_882073.1. NC_002929.2.
3D structure databases
HSSP	HSSP built from PDB template 1B04 based on UniProtKB O87703.
ProteinModelPortal	Q7VRX7.
SMR	Q7VRX7. Positions 9-614.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	2665183.
GenomeReviews	Gene locus BP3560 in contig BX470248_GR.
KEGG	bpe:BP3560.
NMPDR	fig\|257313.1.peg.3143.
PATRIC	21160776. VBIBorPer7866_3853.
Phylogenomic databases
HOGENOM	HBG620317.
OMA	ENVRTIR.
PhylomeDB	Q7VRX7.
ProtClustDB	CLSK2516705.
Enzyme and pathway databases
BioCyc	BPER257313:BP3560-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.
KO	K01972.
Pfam	PF00533. BRCT. 1 hit. PF01653. DNA_ligase_aden. 2 hits. 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. 4 hits. 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. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLJ_BORPE

Accession

Primary (citable) accession number: Q7VRX7

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	October 1, 2003
Last modified:	January 25, 2012
This is version 56 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

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents