DNA ligase - Acidobacterium capsulatum (strain ATCC 51196 / DSM 11244 / JCM 7670)

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:	ACP_1809

Organism

Acidobacterium capsulatum (strain ATCC 51196 / DSM 11244 / JCM 7670) [Complete proteome] [HAMAP]

Taxonomic identifier

240015 [NCBI]

Taxonomic lineage

Bacteria › Acidobacteria › Acidobacteriales › Acidobacteriaceae › Acidobacterium

Protein attributes

Sequence length	677 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 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 – 677

677

DNA ligase HAMAP MF_01588

PRO_0000380279

Regions

Domain

596 – 677

82

BRCT

Nucleotide binding

34 – 38

5

NAD By similarity

Nucleotide binding

83 – 84

2

NAD By similarity

Sites

Active site

117

1

N6-AMP-lysine intermediate By similarity

Metal binding

416

1

Zinc By similarity

Metal binding

419

1

Zinc By similarity

Metal binding

434

1

Zinc By similarity

Metal binding

439

1

Zinc By similarity

Binding site

115

1

NAD By similarity

Binding site

138

1

NAD By similarity

Binding site

180

1

NAD By similarity

Binding site

297

1

NAD By similarity

Binding site

321

1

NAD By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

C1F7S7 [UniParc].

Last modified May 26, 2009. Version 1.
Checksum: F5A2B9569ED50605
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FASTA

677

74,883

        10         20         30         40         50         60 
MSHASAAQQI ESLRESIRHH EYLYYVQDQP EIDDLAFDEL MRKLQRLEAE HPELITPDSP 

        70         80         90        100        110        120 
TQRVGGKPKE GFAKVAHSRP MLSLDNVNSE EELRDWERRV REQAGQNAEI EYVCEYKLDG 

       130        140        150        160        170        180 
LSMALHYRDG QLARGLTRGD GEIGEDVTTN VRTIRSVPLS IADGKLQQAK MPANFEVRGE 

       190        200        210        220        230        240 
VVMPFTAFEK LNEEREAQGL APAANPRNAA AGTIRTLEPN IVAQRRLDFY AYFALTEKGE 

       250        260        270        280        290        300 
DAFGEQEEAL DALATLGFRV NQHRHAAKSI ETVVEFVNRA EEHRSRLGYE IDGVVVKVNS 

       310        320        330        340        350        360 
AVLQRRLGYT GRAPRWAVAY KFAARSGVTQ VEDIQVQVGR TGKLTPVAWL APVQVGGTTV 

       370        380        390        400        410        420 
TRATLHNADE IERLGLRIGD FVRIERGGDV IPKVVEVVDD AEHPRGTKHF HFPHACPACG 

       430        440        450        460        470        480 
SEVVRTPGEA DYRCVNTDCP ARLRESLLHF ASRGVMNIEG MGEAIVMQLL GRGLVKTVSD 

       490        500        510        520        530        540 
IYSLTEEQLV SLERMGKKSA TALLGEIDKS RQAPLDRVLF GLGIRFVGER TAQALAEEYG 

       550        560        570        580        590        600 
SMDALMQASR EELERVNDVG PRVSEAIREF FDEPRNRDLV ERLREAGLRF TGEKRKKTSQ 

       610        620        630        640        650        660 
LAGLTFVLTG TLPGLSRDEA KGKIENAGGH VSGSVSKKTN YVVAGADAGS KLEKANSLGV 

       670 
PVIDEAALIK MLETEQA

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References

[1]

"Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils."
Ward N.L., Challacombe J.F., Janssen P.H., Henrissat B., Coutinho P.M., Wu M., Xie G., Haft D.H., Sait M., Badger J., Barabote R.D., Bradley B., Brettin T.S., Brinkac L.M., Bruce D., Creasy T., Daugherty S.C., Davidsen T.M.

Kuske C.R.
Appl. Environ. Microbiol. 75:2046-2056(2009) [PubMed: 19201974] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 51196 / DSM 11244 / JCM 7670.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001472 Genomic DNA. Translation: ACO32726.1.
RefSeq	YP_002754883.1. NC_012483.1.
3D structure databases
ProteinModelPortal	C1F7S7.
ModBase	Search...
Protein-protein interaction databases
STRING	C1F7S7.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	7700355.
GenomeReviews	Gene locus ACP_1809 in contig CP001472_GR.
KEGG	aca:ACP_1809.
PATRIC	20666907. VBIAciCap40988_1740.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	ENVRTIR.
ProtClustDB	CLSK775239.
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. 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]
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_ACIC5

Accession

Primary (citable) accession number: C1F7S7

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 28, 2009
Last sequence update:	May 26, 2009
Last modified:	January 25, 2012
This is version 22 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

Family and domain databases

Entry information

Relevant documents