DNA ligase - Frankia sp. (strain CcI3)

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:	Francci3_3647

Organism

Frankia sp. (strain CcI3) [Complete proteome] [HAMAP]

Taxonomic identifier

106370 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Frankineae › Frankiaceae › Frankia

Protein attributes

Sequence length	706 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 – 706

706

DNA ligase HAMAP MF_01588

PRO_0000313245

Regions

Domain

604 – 694

91

BRCT

Nucleotide binding

50 – 54

5

NAD By similarity

Nucleotide binding

99 – 100

2

NAD By similarity

Sites

Active site

130

1

N6-AMP-lysine intermediate By similarity

Metal binding

422

1

Zinc By similarity

Metal binding

425

1

Zinc By similarity

Metal binding

440

1

Zinc By similarity

Metal binding

446

1

Zinc By similarity

Binding site

128

1

NAD By similarity

Binding site

151

1

NAD By similarity

Binding site

188

1

NAD By similarity

Binding site

304

1

NAD By similarity

Binding site

328

1

NAD By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q2J6U3 [UniParc].

Last modified March 7, 2006. Version 1.
Checksum: 3E2E9C029CA3B63A
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FASTA

706

75,837

        10         20         30         40         50         60 
MSATAGTADE SGVASAAASA DERARAASLA RELDEHAYRY YVLDSPTISD AEYDRLMAEL 

        70         80         90        100        110        120 
AALEERHPDL RTPDSPTQKV AGSYSTLFTP VEHLERMLSL ENVFDDDEFH QWAARVARES 

       130        140        150        160        170        180 
EVDAWLCELK IDGLAVDLVY EDGYLVRAAT RGDGRTGEDI TPNIRTLASV PVRLRGPRVP 

       190        200        210        220        230        240 
GLLEVRGEVF FPTAKFAELN AGLVAVGGKP FANPRNAAAG SLRQKDPRVT ATRPLEMIVH 

       250        260        270        280        290        300 
GLGAQRGFEV TSQSAAYARF AELGLPVATH FEVLATVPGV LDYVHRWGDA RHDVVHEIDG 

       310        320        330        340        350        360 
VVVKVDSFAL QRRLGSTSKS PRWAVAYKYP PEEVTTKLRD IRVNVGRTGR VTPFGELEPV 

       370        380        390        400        410        420 
LVAGSTVGLA TLHNIDEVGR KGVLIGDTVV LRKAGDVIPE IVGPVVDLRE GSERAFVMPT 

       430        440        450        460        470        480 
RCPECGTELV RPEGEVDIRC PNTVSCPAQL RESIFHFASR GAMDIDGLGY ETATALLEAG 

       490        500        510        520        530        540 
RVRDIGDIFH LTPESFEGLR GFAQKKIDQI LRGVEAARHR PLWRLLVGLS IRHVGPTAAR 

       550        560        570        580        590        600 
ALARELRSLE AIAATSAEDL AAVEGVGPKI AGAVLDWFAD ERHRDILARI AAGGARLADV 

       610        620        630        640        650        660 
GAEEGPRPLD GVTVVITGTL TDWSRDSAKE AVEARGGKVT GSVSRKTTAV VVGADPGASK 

       670        680        690        700 
YDKARSLRIP MLDEAGFAVL LAQGVDAASK LAVPADGPEK AETPVE

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References

[1]

"Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography."
Normand P., Lapierre P., Tisa L.S., Gogarten J.P., Alloisio N., Bagnarol E., Bassi C.A., Berry A.M., Bickhart D.M., Choisne N., Couloux A., Cournoyer B., Cruveiller S., Daubin V., Demange N., Francino M.P., Goltsman E., Huang Y.

Benson D.R.
Genome Res. 17:7-15(2007) [PubMed: 17151343] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CcI3.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000249 Genomic DNA. Translation: ABD12999.1.
RefSeq	YP_482728.1. NC_007777.1.
3D structure databases
ProteinModelPortal	Q2J6U3.
SMR	Q2J6U3. Positions 20-332.
ModBase	Search...
Protein-protein interaction databases
STRING	Q2J6U3.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	3905328.
GenomeReviews	Gene locus Francci3_3647 in contig CP000249_GR.
KEGG	fra:Francci3_3647.
PATRIC	21930732. VBIFraSp10456_3974.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0272.
HOGENOM	HBG620317.
OMA	ENVRTIR.
PhylomeDB	Q2J6U3.
ProtClustDB	CLSK2516647.
Enzyme and pathway databases
BioCyc	FSP106370:FRANCCI3_3647-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. 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_FRASC

Accession

Primary (citable) accession number: Q2J6U3

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	March 7, 2006
Last modified:	January 25, 2012
This is version 46 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