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InterPro: IPR013839 NAD-dependent DNA ligase, adenylation

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2035 proteins

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Accession

IPR013839 DNAligase_adenylation

Secondary

IPR001679

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Pfam	PF01653	DNA_ligase_aden	2035
Signatures in BioMart

InterPro Relationships Help

Found in

IPR001679 NAD-dependent DNA ligase
IPR013840 NAD-dependent DNA ligase, N-terminal
IPR020923 DNA ligase B

Contains

IPR018239 NAD-dependent DNA ligase, active site

GO Term annotation Help

Function

GO:0003911 DNA ligase (NAD+) activity

InterPro annotation

Entry Details in BioMart

Abstract

DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (EC:6.5.1.1), the other NAD (EC:6.5.1.2).

This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [1, 2]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [3, 4].

Structural links Help

PDB - click here

SCOP: b.40.4.6 , d.142.2.2

CATH: 1.10.287.610 , 3.30.1490.70 , 3.30.470.30

Database links Help

Enzyme: EC:6.5.1.2

PRIAM: PRI001843

Pfam Clan: CL0078.9

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR013839

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

A2C5E6 DNA ligase

B9LU22 DNA ligase

O87703 DNA ligase

P72588 DNA ligase

Q197A8 Putative DNA ligase 052L

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR001679	NAD-dependent DNA ligase
IPR003583	Helix-hairpin-helix DNA-binding motif, class 1
IPR004149	Zinc-finger, NAD-dependent DNA ligase C4-type
IPR010994	RuvA domain 2-like
IPR013839	NAD-dependent DNA ligase, adenylation
IPR004150	NAD-dependent DNA ligase, OB-fold
IPR016027	Nucleic acid-binding, OB-fold-like
IPR012340	Nucleic acid-binding, OB-fold
IPR018239	NAD-dependent DNA ligase, active site
IPR001357	BRCT
IPR013840	NAD-dependent DNA ligase, N-terminal
	PDB Chain
	ModBase
	CATH Domain
	SWISS-MODEL
	SCOP Domain

Publications Open in usermanual
1.	Shark KB, Conway T. Cloning and molecular characterization of the DNA ligase gene (lig) from Zymomonas mobilis. FEMS Microbiol. Lett. 75 19-26 1992 [PubMed: 1526462] http://dx.doi.org/10.1016/0378-1097(92)90450-3
2.	Gentry D, Bengra C, Ikehara K, Cashel M. Guanylate kinase of Escherichia coli K-12. J. Biol. Chem. 268 14316-21 1993 [PubMed: 8390989] http://intl.jbc.org/cgi/reprint/268/19/14316.pdf
3.	Singleton MR, Hakansson K, Timson DJ, Wigley DB. Structure of the adenylation domain of an NAD+-dependent DNA ligase. Structure 7 35-42 1999 [PubMed: 10368271] http://dx.doi.org/10.1016/S0969-2126(99)80007-0
4.	Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. EMBO J. 19 1119-29 2000 [PubMed: 10698952] http://dx.doi.org/10.1093/emboj/19.5.1119

Additional Reading Open in usermanual
	Gajiwala KS, Pinko C. Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal. Structure 12 2004 1449-59 [PubMed: 15296738] http://dx.doi.org/10.1016/j.str.2004.05.017
	Lim JH, Choi J, Kim W, Ahn BY, Han YS. Mutational analyses of Aquifex pyrophilus DNA ligase define essential domains for self-adenylation and DNA binding activity. Arch. Biochem. Biophys. 388 2001 253-60 [PubMed: 11368162] http://dx.doi.org/10.1006/abbi.2001.2291

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