DNA ligase 2 - Streptomyces coelicolor

Preferred order of sections

Names and origin

Protein names

Recommended name:
DNA ligase 2
EC=6.5.1.2

Alternative name(s):
Polydeoxyribonucleotide synthase [NAD+] 2

Gene names

Name:	ligA2
Ordered Locus Names:	SCO7522
ORF Names:	SCBAC25F8.14c

Organism

Streptomyces coelicolor

Taxonomic identifier

1902 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Streptomycineae › Streptomycetaceae › Streptomyces

Protein attributes

Sequence length	700 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.
Sequence caution	The sequence CAC42149.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	DNA damage DNA repair DNA replication
Ligand	Magnesium Manganese Metal-binding NAD Zinc
Molecular function	Ligase
Technical term	Complete proteome Reference 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 – 700

700

DNA ligase 2 HAMAP MF_01588

PRO_0000313474

Regions

Domain

615 – 700

86

BRCT

Nucleotide binding

42 – 46

5

NAD By similarity

Nucleotide binding

89 – 90

2

NAD By similarity

Sites

Active site

122

1

N6-AMP-lysine intermediate By similarity

Metal binding

421

1

Zinc By similarity

Metal binding

424

1

Zinc By similarity

Metal binding

437

1

Zinc By similarity

Metal binding

443

1

Zinc By similarity

Binding site

143

1

NAD By similarity

Binding site

177

1

NAD By similarity

Binding site

303

1

NAD By similarity

Binding site

327

1

NAD By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q93IZ8 [UniParc].

Last modified January 15, 2008. Version 2.
Checksum: 7A3B79C11D22E402
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FASTA

700

73,777

        10         20         30         40         50         60 
MIRAMTTPAA VIVDATAYAQ AVEDAAHAAA AYYAGGSSPL DDDAYDRLAR GIAAWEAEHP 

        70         80         90        100        110        120 
DEVLPDSPTG KVAGGAAEGD VPHTVPMLSL DNVFSPEEFT VWTASLARRI DREVTRFSVG 

       130        140        150        160        170        180 
PKLDGLAVAA RYREGRLTRL ITRGDGTAGE DVSHAIGTVE GLPGTLAEPV TVEVRGEILM 

       190        200        210        220        230        240 
TTAQFEHANE VRIRHGGQPF ANPRNAAAGT LRAKERAYTV PMTFFGYGLL ALPGTDAALA 

       250        260        270        280        290        300 
GRLEELPYSE LMETAAGLGV HTSAGTAVPD VVVGTPEQVV ARVQEIAALR AELPFGIDGI 

       310        320        330        340        350        360 
VVKADLAADR RAAGSGSRAP RWAIAYKLPA VEKITRLLEV EWNVGRTGII APRGVLEPVV 

       370        380        390        400        410        420 
IEGSTITYAT LHNPADITRR GLRLGDHVMV HRAGDVIPRI EAPVAHLRTG EEQPIVFPEA 

       430        440        450        460        470        480 
CPRCGSDIDT SEERWRCAQG RNCHLVASLA YAAGRDQLDI EGLGTTRVVQ LVEAGLVADL 

       490        500        510        520        530        540 
ADLFLLRREQ LLALERMGET STDNLLAALA RAKEQPLSRV LCALGVRGTG RSMSRRIARY 

       550        560        570        580        590        600 
FATMDHIRAA DAEAMQRVDG IGVEKAPSVV AEIAELAPLI DRLAAAGVNM TEPGATPPRP 

       610        620        630        640        650        660 
ADTDGADGAT AEAPGDGGPL AGMKVVVTGA MTGNLERLSR NEMNELIERA GGRSSSSVSK 

       670        680        690        700 
NTSLVVAGEG AGSKRAKAEQ LGVRLATPEE FAVLVAGLLS

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References

[1]

"Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)."
Bentley S.D., Chater K.F., Cerdeno-Tarraga A.-M., Challis G.L., Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D., Bateman A., Brown S., Chandra G., Chen C.W., Collins M., Cronin A., Fraser A., Goble A.

Hopwood D.A.
Nature 417:141-147(2002) [PubMed: 12000953] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC BAA-471 / A3(2) / M145.

+

Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AL939131 Genomic DNA. Translation: CAC42149.1. Different initiation.
RefSeq	NP_631567.1. NC_003888.3.
3D structure databases
HSSP	HSSP built from PDB template 1B04 based on UniProtKB O87703.
ProteinModelPortal	Q93IZ8.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1102960.
GenomeReviews	Gene locus SCO7522 in contig AL645882_GR.
KEGG	sco:SCO7522.
NMPDR	fig\|100226.1.peg.7453.
PATRIC	23744987. VBIStrCoe124346_7636.
Phylogenomic databases
HOGENOM	HBG620317.
PhylomeDB	Q93IZ8.
ProtClustDB	CLSK2303633.
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. [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. [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. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLJ2_STRCO

Accession

Primary (citable) accession number: Q93IZ8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	January 15, 2008
Last modified:	January 25, 2012
This is version 63 of the entry and version 2 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

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents