PDBsum entry: 1b04

Ligase

PDB id: 1b04

Contents

Protein chains

310 a.a. *

Waters ×190

* Residue conservation analysis

PDB id:

1b04

Name:

Ligase

Title:

Structure of the adenylation domain of an NAD+ dependent ligase

Structure:

Protein (DNA ligase). Chain: a, b. Fragment: adenylation domain. Engineered: yes. Mutation: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Strain: nca 1503. Gene: lig. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.80Å R-factor: 0.230 R-free: 0.310

Authors:

M.R.Singleton,K.Hakansson,D.J.Timson,D.B.Wigley

Key ref:

M.R.Singleton et al. (1999). Structure of the adenylation domain of an NAD+-dependent DNA ligase. Structure, 7, 35-42. PubMed id: 10368271 DOI: 10.1016/S0969-2126(99)80007-0

Date:

16-Nov-98 Release date: 22-Nov-99

Protein chains

O87703  (DNLJ_GEOSE) -  DNA ligase

Seq: 670 a.a.

Struc: 310 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.6.5.1.2 - Dna ligase (NAD(+)).
• Reaction: NAD⁺ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + nicotinamide nucleotide + (deoxyribonucleotide)(n+m)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biochemical function: DNA ligase (NAD+) activity (1 term)

reference

DOI no: 10.1016/S0969-2126(99)80007-0

Structure 7:35-42 (1999)

PubMed id: 10368271

Structure of the adenylation domain of an NAD+-dependent DNA ligase.

M.R.Singleton, K.Håkansson, D.J.Timson, D.B.Wigley.

ABSTRACT

BACKGROUND: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target. RESULTS: The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 A resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site. CONCLUSIONS: Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.

Selected figure(s)

Figure 5.
Figure 5. Molecular surface of the adenylation domain overlaid with the model for NAD^+ binding. This figure was prepared using GRASP [11].

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 35-42) copyright 1999.

Figure was selected by an automated process.