C1CKI0 (DNLJ_STRZP) Reviewed, UniProtKB/Swiss-Prot

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:	SPP_1122

Organism

Streptococcus pneumoniae (strain P1031) [Complete proteome] [HAMAP]

Taxonomic identifier

488223 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Lactobacillales › Streptococcaceae › Streptococcus › Streptococcus pneumoniae

Protein attributes

Sequence length	652 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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-Rule MF_01588
Catalytic activity	NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m). HAMAP-Rule MF_01588
Cofactor	Magnesium or manganese By similarity. HAMAP-Rule 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	3D-structure 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
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (NAD+) activity Inferred from electronic annotation. Source: HAMAP 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 – 652

652

DNA ligase HAMAP-Rule MF_01588

PRO_0000380487

Regions

Domain

577 – 652

76

BRCT

Nucleotide binding

29 – 33

5

NAD By similarity

Nucleotide binding

78 – 79

2

NAD By similarity

Sites

Active site

109

1

N6-AMP-lysine intermediate By similarity

Metal binding

395

1

Zinc By similarity

Metal binding

398

1

Zinc By similarity

Metal binding

413

1

Zinc By similarity

Metal binding

418

1

Zinc By similarity

Binding site

107

1

NAD By similarity

Binding site

130

1

NAD By similarity

Binding site

164

1

NAD By similarity

Binding site

278

1

NAD By similarity

Binding site

302

1

NAD By similarity

Secondary structure

1

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652

Helix Strand Turn

Details...

Helix

3 – 6

4

Helix

38 – 45

8

Helix

47 – 49

3

Helix

55 – 58

4

Beta strand

68 – 71

4

Helix

85 – 95

11

Turn

96 – 98

3

Beta strand

104 – 110

7

Beta strand

112 – 120

9

Beta strand

123 – 129

7

Beta strand

133 – 138

6

Helix

140 – 143

4

Beta strand

159 – 166

8

Helix

169 – 181

13

Helix

190 – 198

9

Beta strand

199 – 202

4

Helix

203 – 208

6

Beta strand

212 – 221

10

Beta strand

223 – 226

4

Helix

227 – 237

11

Beta strand

246 – 250

5

Helix

251 – 264

14

Helix

265 – 267

3

Beta strand

268 – 270

3

Beta strand

272 – 279

8

Helix

282 – 288

7

Beta strand

292 – 302

11

Sequences

	Sequence		Length	Mass (Da)
	C1CKI0 [UniParc]. Last modified May 26, 2009. Version 1. Checksum: C2220D1F3504D47B	FASTA	652	72,276
	10 20 30 40 50 60 MNKRMNELVA LLNRYATEYY TSDNPSVSDS EYDRLYRELV ELETAYPEQV LADSPTHRVG 70 80 90 100 110 120 GKVLDGFEKY SHQYPLYSLQ DAFSREELDA FDARVRKEVA HPTYICELKI DGLSISLTYE 130 140 150 160 170 180 KGILVAGVTR GDGSIGENIT ENLKRVKDIP LTLPEELDIT VRGECYMPRA SFDQVNQARQ 190 200 210 220 230 240 ENGEPEFANP RNAAAGTLRQ LDTAVVAKRN LATFLYQEAS PSTRDSQEKG LKYLEQLGFV 250 260 270 280 290 300 VNPKRILAEN IDEIWNFIQE VGQERENLPY DIDGVVIKVN DLASQEELGF TVKAPKWAVA 310 320 330 340 350 360 YKFPAEEKEA QLLSVDWTVG RTGVVTPTAN LTPVQLAGTT VSRATLHNVD YIAEKDIRKD 370 380 390 400 410 420 DTVIVYKAGD IIPAVLRVVE SKRVSEEKLD IPTNCPSCNS DLLHFEDEVA LRCINPRCPA 430 440 450 460 470 480 QIMEGLIHFA SRDAMNITGL GPSIVEKLFA ANLVKDVADI YRLQEEDFLL LEGVKEKSAA 490 500 510 520 530 540 KLYQAIQASK ENSAEKLLFG LGIRHVGSKA SQLLLQYFHS IENLYQADSE EVASIESLGG 550 560 570 580 590 600 VIAKSLQTYF ATEGSEILLR ELKETGVNLD YKGQTVVADA ALSGLTVVLT GKLERLKRSE 610 620 630 640 650 AKSKLESLGA KVTGSVSKKT DLVVVGADAG SKLQKAQELG IQVRDEAWLE SL

References

[1]	"Complete genome sequence of Streptococcus pneumoniae strain P1031." Hotopp J.D., Censini S., Masignani V., Covacci A., Tettelin H. Submitted (DEC-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: P1031.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

CP000920 Genomic DNA. Translation: ACO21382.1.

RefSeq

YP_002738268.1. NC_012467.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4GLW	X-ray	2.00	A/B	1-305	[»]

ProteinModelPortal

C1CKI0.

SMR

C1CKI0. Positions 2-304.

ModBase

Search...

Protein-protein interaction databases

STRING

488223.SPP_1122.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ACO21382; ACO21382; SPP_1122.

GeneID

7682167.

KEGG

spp:SPP_1122.

PATRIC

32459541. VBIStrPne91701_1167.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG0272.

HOGENOM

HOG000218458.

KO

K01972.

OMA

ENVRTIR.

ProtClustDB

PRK07956.

Enzyme and pathway databases

BioCyc

SPNE488223:GHE7-1100-MONOMER.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.

HAMAP

MF_01588. DNA_ligase_A.

InterPro

IPR001357. BRCT_dom.
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.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]

PANTHER

PTHR11107:SF5. PTHR11107:SF5. 1 hit.

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. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DNLJ_STRZP

Accession

Primary (citable) accession number: C1CKI0

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 28, 2009
Last sequence update:	May 26, 2009
Last modified:	May 29, 2013
This is version 36 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program