DNA ligase - Leifsonia xyli subsp. xyli (strain CTCB07)

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:	Lxx14380

Organism

Leifsonia xyli subsp. xyli (strain CTCB07) [Complete proteome] [HAMAP]

Taxonomic identifier

281090 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Micrococcineae › Microbacteriaceae › Leifsonia

Protein attributes

Sequence length	747 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 – 747

747

DNA ligase HAMAP MF_01588

PRO_0000313289

Regions

Domain

659 – 747

89

BRCT

Nucleotide binding

33 – 37

5

NAD By similarity

Nucleotide binding

83 – 84

2

NAD By similarity

Sites

Active site

115

1

N6-AMP-lysine intermediate By similarity

Metal binding

417

1

Zinc By similarity

Metal binding

420

1

Zinc By similarity

Metal binding

436

1

Zinc By similarity

Metal binding

442

1

Zinc By similarity

Binding site

113

1

NAD By similarity

Binding site

136

1

NAD By similarity

Binding site

174

1

NAD By similarity

Binding site

299

1

NAD By similarity

Binding site

323

1

NAD By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q6AEE5 [UniParc].

Last modified September 13, 2004. Version 1.
Checksum: 2502530C68F9DF52
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FASTA

747

80,467

        10         20         30         40         50         60 
MAADARAEAQ GLTTRILELR DAYYELDTVL VSDEEYDRML RRLEELERLH PELQSQDSPT 

        70         80         90        100        110        120 
QTVGGRAQTT LFAPVEHAER MLSLDNVFSF EAFEAWAAKI ERDAGRRVDY LCELKIDGLA 

       130        140        150        160        170        180 
INLRYENGVL VTAATRGDGV VGEDVTENIR HIPAITQRLS GAGPFPPVVE VRGEVFFPVA 

       190        200        210        220        230        240 
KFEELNANQQ AAGERVFANA RNAASGSLRQ KAEGKNPAQR RLMRDRLGRL RMLVHGIGAW 

       250        260        270        280        290        300 
PNPPVATQSG VYELLRSWGL PTSAHGRVFG TVQEAADFIG RSAERRDTVE HEIDGVVIKV 

       310        320        330        340        350        360 
DELVLHDELG ATSRAPRWAI AYKYPPEQVN TKLLDIVVSV GRTGRATPFA VMEKVKVAGS 

       370        380        390        400        410        420 
EVRQATLHNQ DVVKAKGVLI GDTVVLRKAG DVIPEVLGPV VELRDGTERE FAMPTDCPEC 

       430        440        450        460        470        480 
GTPLAPAKEG DIDLRCPNAE FCPAQVRGRV EHIGSRGGLD IEALGEVAAA ALTQPRFPER 

       490        500        510        520        530        540 
APLPTEAGLF GLRLEDLFPI EVVVRDSETG LPKLTETGVE KVDAPFRRRR QKKDGAFDPE 

       550        560        570        580        590        600 
AEAFDGDEIA VPSKSAIELL ANLRAARTKP LWRILVSLNI RHVGPVAARA LADHFGSLDA 

       610        620        630        640        650        660 
IRAASRDELA AVDGVGGIVA DAVLSWFEIG WHCEIVENWA RDGVQFAIPG HPGPGRADTG 

       670        680        690        700        710        720 
GGVLSGLTVV ATGSLEGYTR EAAQEAIVAA GGKAASSVSK KTDFVAAGPG AGSKLAKAEE 

       730        740 
LGVRVLDAAQ FTILVEQGPG ALPEVAE

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References

[1]

"The genome sequence of the Gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli."
Monteiro-Vitorello C.B., Camargo L.E.A., Van Sluys M.A., Kitajima J.P., Truffi D., do Amaral A.M., Harakava R., de Oliveira J.C.F., Wood D., de Oliveira M.C., Miyaki C.Y., Takita M.A., da Silva A.C.R., Furlan L.R., Carraro D.M., Camarotte G., Almeida N.F. Jr., Carrer H.

Setubal J.C.
Mol. Plant Microbe Interact. 17:827-836(2004) [PubMed: 15305603] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CTCB07.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE016822 Genomic DNA. Translation: AAT89251.1.
RefSeq	YP_062356.2. NC_006087.1.
3D structure databases
HSSP	HSSP built from PDB template 1ZAU based on UniProtKB P63973.
ProteinModelPortal	Q6AEE5.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	2938486.
GenomeReviews	Gene locus Lxx14380 in contig AE016822_GR.
KEGG	lxx:Lxx14380.
NMPDR	fig\|281090.3.peg.873.
PATRIC	22336504. VBILeiXyl11655_1494.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG620317.
OMA	ENVRTIR.
ProtClustDB	PRK07956.
Enzyme and pathway databases
BioCyc	LXYL281090:LXX14380-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. 2 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. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLJ_LEIXX

Accession

Primary (citable) accession number: Q6AEE5

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	September 13, 2004
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

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents