DNA ligase - Frankia alni (strain ACN14a)

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:	FRAAL5859

Organism

Frankia alni (strain ACN14a) [Complete proteome] [HAMAP]

Taxonomic identifier

326424 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	771 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 – 771

771

DNA ligase HAMAP MF_01588

PRO_0000313244

Regions

Domain

641 – 731

91

BRCT

Nucleotide binding

87 – 91

5

NAD By similarity

Nucleotide binding

136 – 137

2

NAD By similarity

Sites

Active site

167

1

N6-AMP-lysine intermediate By similarity

Metal binding

459

1

Zinc By similarity

Metal binding

462

1

Zinc By similarity

Metal binding

477

1

Zinc By similarity

Metal binding

483

1

Zinc By similarity

Binding site

165

1

NAD By similarity

Binding site

188

1

NAD By similarity

Binding site

225

1

NAD By similarity

Binding site

341

1

NAD By similarity

Binding site

365

1

NAD By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q0RDH8 [UniParc].

Last modified September 5, 2006. Version 1.
Checksum: 6D619F5F0C48EBC8
Show »

FASTA

771

81,427

        10         20         30         40         50         60 
MNAPPGSGDA AASALEAASQ AEASEVEASE AEAASAVEAA SAVGAGGAVQ PAVAASVADR 

        70         80         90        100        110        120 
ARAAELAREL DEHAYRYYVL DSPTVSDAEY DRLMRELTAL EEHHPELRTP DSPTQKVAGS 

       130        140        150        160        170        180 
YSTLFTPVEH LERLLSLDNV FDDDEFHLWA ARAARETEVD GWLCELKIDG LAVDLVYEEG 

       190        200        210        220        230        240 
RLVRAATRGD GRTGEDITPN IRTLASVPTR LRGASVPELL EVRGEVFFPT EKFAELNASL 

       250        260        270        280        290        300 
VAGGGKPFAN PRNAAAGSLR QKDPRVTATR PLDMIVHGLG AQRGFDAASQ SAAYARFAEF 

       310        320        330        340        350        360 
GLPVSTHFEV LASVGDVLAF IHRWGRARHD VEHEIDGVVV KVDAFALQRR LGSTSKAPRW 

       370        380        390        400        410        420 
AVAFKYPPEE VTTKLRDIRV NVGRTGRVTP FGELEPVLVA GSTVGLATLH NVDEVGRKGV 

       430        440        450        460        470        480 
LIGDTVVLRK AGDVIPEIVG PVVDLRDGTE RAFVMPTHCP ECGTELVRPE GEVDIRCPNT 

       490        500        510        520        530        540 
DACPAQLREL IFHLASRNAL DIDGLGYETA IALLEADRVG DIGDIFHLTP ESFEGLRGFG 

       550        560        570        580        590        600 
QKKIDQILRG VEAARHRPLW RLLVGLSIRH VGPTAARALA RELRSLDAIA AAPAEQLAAV 

       610        620        630        640        650        660 
EGVGPKIASA VVDWFADARH RDIVARIAAG GASLADAGAA EGPRPLDGVA VVITGTLDGW 

       670        680        690        700        710        720 
SRDSATEAVQ GRGGKVTGSV SKKTAFVVVG ADPGAAKYDK ARSLGVPVLD EAGFAVLLER 

       730        740        750        760        770 
GADAARERAV AADAPAAPAA PDTSGGQGAP DVDSARRAQR AQRAQDDAPP G

« Hide

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: ACN14a.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CT573213 Genomic DNA. Translation: CAJ64491.1.
RefSeq	YP_716010.1. NC_008278.1.
3D structure databases
ProteinModelPortal	Q0RDH8.
SMR	Q0RDH8. Positions 66-369.
ModBase	Search...
Protein-protein interaction databases
STRING	Q0RDH8.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	4237485.
GenomeReviews	Gene locus FRAAL5859 in contig CT573213_GR.
KEGG	fal:FRAAL5859.
PATRIC	21920846. VBIFraAln347_5370.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0272.
HOGENOM	HBG620317.
OMA	ENVRTIR.
PhylomeDB	Q0RDH8.
ProtClustDB	CLSK2516647.
Enzyme and pathway databases
BioCyc	FALN326424:FRAAL5859-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_FRAAA

Accession

Primary (citable) accession number: Q0RDH8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	September 5, 2006
Last modified:	January 25, 2012
This is version 41 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