Reviewed, UniProtKB/Swiss-Prot P56709 (DNLI_PYRFU)

Names and origin

Protein names

Recommended name:
    DNA ligase
    EC=6.5.1.1
Alternative name(s):
    Polydeoxyribonucleotide synthase [ATP]
    Pfu DNA ligase

Gene names

Name:	lig
Ordered Locus Names:	PF1635

Organism

Pyrococcus furiosus [Complete proteome] [HAMAP]

Taxonomic identifier

2261 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	561 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. HAMAP MF_00407
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). Ref.3
Cofactor	Magnesium Probable.
Subunit structure	Monomer. HAMAP MF_00407
Sequence similarities	Belongs to the ATP-dependent DNA ligase family.
Biophysicochemical properties	Temperature dependence: Optimum temperature is about 70 degrees Celsius. Active from 4 to 100 degrees Celsius. Thermostable. HAMAP MF_00407

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	DNA recombination Inferred from electronic annotation. Source: HAMAP DNA repair Inferred from electronic annotation. Source: HAMAP DNA replication Inferred from electronic annotation. Source: HAMAP cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: HAMAP magnesium 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 – 561

561

DNA ligase HAMAP MF_00407

PRO_0000059613

Sites

Active site

249

1

N6-AMP-lysine intermediate Ref.3

Binding site

247

1

ATP HAMAP MF_00407

Binding site

254

1

ATP HAMAP MF_00407

Binding site

269

1

ATP HAMAP MF_00407

Binding site

299

1

ATP HAMAP MF_00407

Binding site

339

1

ATP HAMAP MF_00407

Binding site

414

1

ATP By similarity

Binding site

420

1

ATP HAMAP MF_00407

Experimental info

Mutagenesis

249

1

K → A: Loss of N6-AMP-lysine intermediate. Ref.3

Mutagenesis

531

1

R → A: Reduced ATP binding and enzyme activity; when associated with A-534. Ref.3

Mutagenesis

534

1

K → A: Reduced ATP binding and enzyme activity; when associated with A-531. Ref.3

Secondary structure

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561

Helix Strand Turn

Details...

Helix

3 – 14

12

Helix

19 – 32

14

Helix

35 – 37

3

Turn

38 – 40

3

Helix

41 – 45

5

Helix

62 – 73

12

Helix

77 – 87

11

Helix

90 – 101

12

Turn

102 – 104

3

Helix

113 – 125

13

Beta strand

128 – 130

3

Helix

131 – 143

13

Helix

148 – 159

12

Helix

168 – 178

11

Helix

183 – 193

11

Helix

196 – 213

18

Beta strand

226 – 231

6

Helix

233 – 239

7

Beta strand

244 – 249

6

Beta strand

252 – 260

9

Beta strand

263 – 267

5

Helix

275 – 277

3

Helix

279 – 288

10

Beta strand

291 – 303

13

Beta strand

307 – 309

3

Helix

313 – 320

8

Helix

325 – 331

7

Beta strand

334 – 344

11

Helix

354 – 364

11

Beta strand

369 – 373

5

Beta strand

376 – 380

5

Helix

382 – 394

13

Beta strand

399 – 403

5

Beta strand

414 – 421

8

Beta strand

428 – 437

10

Helix

440 – 442

3

Beta strand

445 – 454

10

Turn

456 – 458

3

Beta strand

461 – 467

7

Helix

473 – 483

11

Helix

484 – 486

3

Beta strand

487 – 491

5

Beta strand

494 – 497

4

Beta strand

502 – 506

5

Beta strand

508 – 511

4

Beta strand

514 – 516

3

Beta strand

521 – 524

4

Beta strand

526 – 530

5

Helix

536 – 538

3

Helix

542 – 557

16

Sequences

	Sequence		Length	Mass (Da)
	P56709-1 [UniParc]. Last modified May 30, 2000. Version 1. Checksum: 534158525B9D24B2	FASTA	561	63,773
	10 20 30 40 50 60 MRYLELAQLY QKLEKTTMKL IKTRLVADFL KKVPDDHLEF IPYLILGEVF PEWDERELGV 70 80 90 100 110 120 GEKLLIKAVA MATGIDAKEI EESVKDTGDL GESIALAVKK KKQKSFFSQP LTIKRVYQTL 130 140 150 160 170 180 VKVAETTGEG SQDKKVKYLA DLFMDAEPLE AKYLARTILG TMRTGVAEGL LRDAIAMAFH 190 200 210 220 230 240 VKVELVERAY MLTSDFGYVA KIAKLEGNEG LAKVQVQLGK PIKPMLAQQA ASIRDALLEM 250 260 270 280 290 300 GGEAEFEIKY DGARVQVHKD GSKIIVYSRR LENVTRAIPE IVEALKEAII PEKAIVEGEL 310 320 330 340 350 360 VAIGENGRPL PFQYVLRRFR RKHNIEEMME KIPLELNLFD VLYVDGQSLI DTKFIDRRRT 370 380 390 400 410 420 LEEIIKQNEK IKVAENLITK KVEEAEAFYK RALEMGHEGL MAKRLDAVYE PGNRGKKWLK 430 440 450 460 470 480 IKPTMENLDL VIIGAEWGEG RRAHLFGSFI LGAYDPETGE FLEVGKVGSG FTDDDLVEFT 490 500 510 520 530 540 KMLKPLIIKE EGKRVWLQPK VVIEVTYQEI QKSPKYRSGF ALRFPRFVAL RDDKGPEDAD 550 560 TIERIAQLYE LQEKMKGKVE S

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Purified thermostable Pyrococcus furiosus DNA ligase." Mathur E.J., Marsh E.J., Schoettlin W.E. Patent number US5700672, 23-DEC-1997 Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF N-TERMINUS. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[2]	"The complete sequence of the Pyrococcus furiosus genome." Weiss R.B., Dunn D.M., Robb F.T., Brown J.R. Submitted (FEB-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[3]	"The closed structure of an archaeal DNA ligase from Pyrococcus furiosus." Nishida H., Kiyonari S., Ishino Y., Morikawa K. J. Mol. Biol. 360:956-967(2006) [PubMed: 16820169] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANT ALA-534 IN COMPLEX WITH AMP, ACTIVE SITE, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF LYS-249; ARG-531 AND LYS-534.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AE010263 Genomic DNA. Translation: AAL81759.1.

RefSeq

NP_579364.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2CFM	X-ray	1.80	A	1-561	[»]

ModBase

Search...

Genome annotation databases

GeneID

1469512.

GenomeReviews

Gene locus PF1635 in contig AE009950_GR.

KEGG

pfu:PF1635.

NMPDR

fig|186497.1.peg.1683.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

P56709.

OMA

P56709. SNLHLGA.

Enzyme and pathway databases

BRENDA

6.5.1.1. 321.

Family and domain databases

HAMAP

MF_00407.
[Tree]

InterPro

IPR000977. DNA_ligase.
IPR012309. DNA_ligase_A_C.
IPR012310. DNA_ligase_A_M.
IPR012308. DNA_ligase_A_N.
IPR016059. DNA_ligase_CS.
IPR012340. NA-bd_OB-fold.
[Graphical view]

Gene3D

G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.

Pfam

PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00574. dnl1. 1 hit.

PROSITE

PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DNLI_PYRFU

Accession

Primary (citable) accession number: P56709

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	May 30, 2000
Last modified:	June 16, 2009
This is version 65 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)