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B0RGA7 (DNLJ_CLAMS) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 30. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
DNA ligase
EC=6.5.1.2
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD+]
Gene names
Name:ligA
Ordered Locus Names:CMS1049
OrganismClavibacter michiganensis subsp. sepedonicus (strain ATCC 33113 / JCM 9667) [Complete proteome] [HAMAP]
Taxonomic identifier31964 [NCBI]
Taxonomic lineageBacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Micrococcineae › Microbacteriaceae › Clavibacter

Protein attributes

Sequence length847 AA.
Sequence statusComplete.
Protein existenceInferred 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 processDNA damage
DNA repair
DNA replication
   LigandMagnesium
Manganese
Metal-binding
NAD
Zinc
   Molecular functionLigase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological processDNA repair

Inferred from electronic annotation. Source: UniProtKB-KW

DNA replication

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentintracellular

Inferred from electronic annotation. Source: InterPro

   Molecular functionDNA 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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 847847DNA ligase HAMAP MF_01588
PRO_0000340338

Regions

Domain686 – 77590BRCT
Nucleotide binding54 – 585NAD By similarity
Nucleotide binding104 – 1052NAD By similarity

Sites

Active site1371N6-AMP-lysine intermediate By similarity
Metal binding4441Zinc By similarity
Metal binding4471Zinc By similarity
Metal binding4631Zinc By similarity
Metal binding4691Zinc By similarity
Binding site1351NAD By similarity
Binding site1581NAD By similarity
Binding site1951NAD By similarity
Binding site3261NAD By similarity
Binding site3501NAD By similarity

Sequences

Sequence LengthMass (Da)Tools
B0RGA7 [UniParc].

Last modified April 8, 2008. Version 1.
Checksum: 3411938F726FDEDC

FASTA84789,734
        10         20         30         40         50         60 
MSDTTTGSDA ADAAVPATTP ADLEAASARV DELRAEIERH RDAYYGETGG TVSDAEYDAL 

        70         80         90        100        110        120 
ERELRAIEDA HPTLRSQDSP TQTVGGRAET TLFAPVTHAE RMLSLDNVFS EEELAEWAAK 

       130        140        150        160        170        180 
VERDAGRGRV RYLSELKIDG LAINLRYEHG VLVTAATRGD GVVGEDVTQN VLTMGTVPER 

       190        200        210        220        230        240 
LAGSGHPPLV EVRGEIFFPV AEFDELNARQ LEVGERVFAN PRNAAAGSLR QKEEGKSPAR 

       250        260        270        280        290        300 
LELMHARIRR LRMLVHGIGA WPVRELERDA HVSAQSEVYG LLEAWGLPIS THFRVFDDIA 

       310        320        330        340        350        360 
EVAGFVRRQG ADRAAVEHQI DGIVVKVDDL GLHEELGATS RAPRWATAYK YPPEEVNTTL 

       370        380        390        400        410        420 
LDIVVSVGRT GRATPFAVME KVEVAGSEVR QATLHNQQVV KAKGVLIGDT VVLRKAGDVI 

       430        440        450        460        470        480 
PEVLGPVVEL RTGKEHEFVM PTLCPECQTP LKPAKEGDID LRCPNARSCP AQVRGRVEHV 

       490        500        510        520        530        540 
ASRGALDIEG LGEVAAAALT QPLEPEDPPL ETEAGLFELT MADLVPITVV VRDAETGMVK 

       550        560        570        580        590        600 
VDEKTGEAKR VTPFRRKRVL KRDGAFDPAE PWGDEASVPS KSAEVLLENL EKAKTQDLWR 

       610        620        630        640        650        660 
ILVALSIRHV GPVAARALAG WFGSLDVIRA ASREELAAVD GVGGIIADAL LDWFEVDWHR 

       670        680        690        700        710        720 
EIVARWEKAG VVTAVPGHPG PGAAAAAGGV LAGLAVVATG SLEGYTREGA LEAIMAAGGK 

       730        740        750        760        770        780 
AGSSVSKKTH YVAAGPGAGS KLGKAEALGV RIIDAAEFRL LVEQGPDAIA LPEADPVPDA 

       790        800        810        820        830        840 
AETAPDGGSA EDATAATAGA AEAATAEAKP KRARKRKAPA AAAAAPPTDV EAGTAVHAEP 


DGPAETP

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References

[1]"Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation."
Bentley S.D., Corton C., Brown S.E., Barron A., Clark L., Doggett J., Harris B., Ormond D., Quail M.A., May G., Francis D., Knudson D., Parkhill J., Ishimaru C.A.
J. Bacteriol. 190:2150-2160(2008) [PubMed: 18192393] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 33113 / JCM 9667.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AM849034 Genomic DNA. Translation: CAQ01163.1.
RefSeqYP_001709792.1. NC_010407.1.

3D structure databases

ProteinModelPortalB0RGA7.
ModBaseSearch...

Protein-protein interaction databases

STRINGB0RGA7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID6159025.
GenomeReviewsGene locus CMS1049 in contig AM849034_GR.
KEGGcms:CMS_1049.
PATRIC21459112. VBIClaMic4666_1117.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHBG620317.
OMAENVRTIR.
ProtClustDBPRK07956.

Enzyme and pathway databases

BioCycCMIC31964:CMS1049-MONOMER.

Family and domain databases

HAMAPMF_01588. DNA_ligase_A.
[Tree]
InterProIPR001357. 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]
Gene3DG3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
KOK01972.
PfamPF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFPIRSF001604. LigA. 1 hit.
SMARTSM00292. BRCT. 1 hit.
SM00278. HhH1. 2 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMSSF52113. BRCT. 1 hit.
SSF50249. Nucleic_acid_OB. 1 hit.
SSF47781. RuvA_2_like. 1 hit.
TIGRFAMsTIGR00575. Dnlj. 1 hit.
PROSITEPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. False negative.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDNLJ_CLAMS
AccessionPrimary (citable) accession number: B0RGA7
Entry history
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: April 8, 2008
Last modified: January 25, 2012
This is version 30 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

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