PDBsum entry 1b04

Go to PDB code: 
protein Protein-protein interface(s) links
Ligase PDB id
Protein chains
310 a.a. *
Waters ×190
* Residue conservation analysis
PDB id:
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.
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
16-Nov-98     Release date:   22-Nov-99    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O87703  (DNLJ_GEOSE) -  DNA ligase
670 a.a.
310 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Dna ligase (NAD(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m)
+ (deoxyribonucleotide)(n)
+ (deoxyribonucleotide)(m)
+ beta-nicotinamide D-ribonucleotide
+ (deoxyribonucleotide)(n+m)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     DNA ligase (NAD+) activity     1 term  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20443037 B.A.Akhoon, S.K.Gupta, G.Dhaliwal, M.Srivastava, and S.K.Gupta (2011).
Virtual screening of specific chemical compounds by exploring E.coli NAD(+)-dependent DNA ligase as a target for antibacterial drug discovery.
  J Mol Model, 17, 265-273.  
19913033 A.Piserchio, P.A.Nair, S.Shuman, and R.Ghose (2010).
Solution NMR studies of Chlorella virus DNA ligase-adenylate.
  J Mol Biol, 395, 291-308.  
19150981 L.K.Wang, H.Zhu, and S.Shuman (2009).
Structure-guided Mutational Analysis of the Nucleotidyltransferase Domain of Escherichia coli DNA Ligase (LigA).
  J Biol Chem, 284, 8486-8494.  
18515356 L.K.Wang, P.A.Nair, and S.Shuman (2008).
Structure-guided Mutational Analysis of the OB, HhH, and BRCT Domains of Escherichia coli DNA Ligase.
  J Biol Chem, 283, 23343-23352.  
18080330 N.Dwivedi, D.Dube, J.Pandey, B.Singh, V.Kukshal, R.Ramachandran, and R.P.Tripathi (2008).
NAD(+)-dependent DNA ligase: a novel target waiting for the right inhibitor.
  Med Res Rev, 28, 545-568.  
18795946 T.I.Meier, D.Yan, R.B.Peery, K.A.McAllister, C.Zook, S.B.Peng, and G.Zhao (2008).
Identification and characterization of an inhibitor specific to bacterial NAD+-dependent DNA ligases.
  FEBS J, 275, 5258-5271.  
17686784 C.Yuan, X.W.Lou, E.Rhoades, H.Chen, and L.A.Archer (2007).
T4 DNA ligase is more than an effective trap of cyclized dsDNA.
  Nucleic Acids Res, 35, 5294-5302.  
17488851 H.Zhu, and S.Shuman (2007).
Characterization of Agrobacterium tumefaciens DNA ligases C and D.
  Nucleic Acids Res, 35, 3631-3645.  
17466627 J.Nandakumar, P.A.Nair, and S.Shuman (2007).
Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate.
  Mol Cell, 26, 257-271.
PDB code: 2owo
17557328 S.K.Srivastava, D.Dube, V.Kukshal, A.K.Jha, K.Hajela, and R.Ramachandran (2007).
NAD+-dependent DNA ligase (Rv3014c) from Mycobacterium tuberculosis: novel structure-function relationship and identification of a specific inhibitor.
  Proteins, 69, 97.  
16476729 D.Akey, A.Martins, J.Aniukwu, M.S.Glickman, S.Shuman, and J.M.Berger (2006).
Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D.
  J Biol Chem, 281, 13412-13423.
PDB code: 1vs0
16481318 M.E.Fraser, K.Hayakawa, M.S.Hume, D.G.Ryan, and E.R.Brownie (2006).
Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.
  J Biol Chem, 281, 11058-11065.
PDB codes: 2fp4 2fpg 2fpi 2fpp
15671015 H.Zhu, and S.Shuman (2005).
Structure-guided mutational analysis of the nucleotidyltransferase domain of Escherichia coli NAD+-dependent DNA ligase (LigA).
  J Biol Chem, 280, 12137-12144.  
15724164 L.Liu, Z.Tang, K.Wang, W.Tan, J.Li, Q.Guo, X.Meng, and C.Ma (2005).
Using molecular beacon to monitor activity of E. coli DNA ligase.
  Analyst, 130, 350-357.  
16153292 M.Stancek, R.Schnell, and M.Rydén-Aulin (2005).
Analysis of Escherichia coli nicotinate mononucleotide adenylyltransferase mutants in vivo and in vitro.
  BMC Biochem, 6, 16.  
16361267 S.K.Srivastava, D.Dube, N.Tewari, N.Dwivedi, R.P.Tripathi, and R.Ramachandran (2005).
Mycobacterium tuberculosis NAD+-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I.
  Nucleic Acids Res, 33, 7090-7101.  
15901723 S.K.Srivastava, R.P.Tripathi, and R.Ramachandran (2005).
NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis. Crystal structure of the adenylation domain and identification of novel inhibitors.
  J Biol Chem, 280, 30273-30281.
PDB code: 1zau
14747344 D.Georlette, V.Blaise, F.Bouillenne, B.Damien, S.H.Thorbjarnardóttir, E.Depiereux, C.Gerday, V.N.Uversky, and G.Feller (2004).
Adenylation-dependent conformation and unfolding pathways of the NAD+-dependent DNA ligase from the thermophile Thermus scotoductus.
  Biophys J, 86, 1089-1104.  
15268945 H.J.Jeon, H.J.Shin, J.J.Choi, H.S.Hoe, H.K.Kim, S.W.Suh, and S.T.Kwon (2004).
Mutational analyses of the thermostable NAD+-dependent DNA ligase from Thermus filiformis.
  FEMS Microbiol Lett, 237, 111-118.  
15565146 J.M.Pascal, P.J.O'Brien, A.E.Tomkinson, and T.Ellenberger (2004).
Human DNA ligase I completely encircles and partially unwinds nicked DNA.
  Nature, 432, 473-478.
PDB code: 1x9n
15296738 K.S.Gajiwala, and C.Pinko (2004).
Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal.
  Structure, 12, 1449-1459.
PDB codes: 1ta8 1tae
15328364 P.Liu, A.Burdzy, and L.C.Sowers (2004).
DNA ligases ensure fidelity by interrogating minor groove contacts.
  Nucleic Acids Res, 32, 4503-4511.  
14523019 D.Georlette, V.Blaise, C.Dohmen, F.Bouillenne, B.Damien, E.Depiereux, C.Gerday, V.N.Uversky, and G.Feller (2003).
Cofactor binding modulates the conformational stabilities and unfolding patterns of NAD(+)-dependent DNA ligases from Escherichia coli and Thermus scotoductus.
  J Biol Chem, 278, 49945-49953.  
12867414 H.Brötz-Oesterhelt, I.Knezevic, S.Bartel, T.Lampe, U.Warnecke-Eberz, K.Ziegelbauer, D.Häbich, and H.Labischinski (2003).
Specific and potent inhibition of NAD+-dependent DNA ligase by pyridochromanones.
  J Biol Chem, 278, 39435-39442.  
12519752 K.L.Carrick, and M.D.Topal (2003).
Amino acid substitutions at position 43 of NaeI endonuclease. Evidence for changes in NaeI structure.
  J Biol Chem, 278, 9733-9739.  
12473094 A.V.Cherepanov, and Vries (2002).
Dynamic mechanism of nick recognition by DNA ligase.
  Eur J Biochem, 269, 5993-5999.  
11751916 V.Sriskanda, and S.Shuman (2002).
Role of nucleotidyl transferase motif V in strand joining by chlorella virus DNA ligase.
  J Biol Chem, 277, 9661-9667.  
11781321 V.Sriskanda, and S.Shuman (2002).
Conserved residues in domain Ia are required for the reaction of Escherichia coli DNA ligase with NAD+.
  J Biol Chem, 277, 9695-9700.  
11442824 A.Wilkinson, J.Day, and R.Bowater (2001).
Bacterial DNA ligases.
  Mol Microbiol, 40, 1241-1248.  
11325928 F.S.Kaczmarek, R.P.Zaniewski, T.D.Gootz, D.E.Danley, M.N.Mansour, M.Griffor, A.V.Kamath, M.Cronan, J.Mueller, D.Sun, P.K.Martin, B.Benton, L.McDowell, D.Biek, and M.B.Schmid (2001).
Cloning and functional characterization of an NAD(+)-dependent DNA ligase from Staphylococcus aureus.
  J Bacteriol, 183, 3016-3024.  
11812821 V.Sriskanda, and S.Shuman (2001).
A second NAD(+)-dependent DNA ligase (LigB) in Escherichia coli.
  Nucleic Acids Res, 29, 4930-4934.  
11058099 A.J.Doherty, and S.W.Suh (2000).
Structural and mechanistic conservation in DNA ligases.
  Nucleic Acids Res, 28, 4051-4058.  
10848966 D.Georlette, Z.O.Jónsson, F.Van Petegem, J.Chessa, J.Van Beeumen, U.Hübscher, and C.Gerday (2000).
A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures.
  Eur J Biochem, 267, 3502-3512.  
10684941 J.Tong, F.Barany, and W.Cao (2000).
Ligation reaction specificities of an NAD(+)-dependent DNA ligase from the hyperthermophile Aquifex aeolicus.
  Nucleic Acids Res, 28, 1447-1454.  
10698952 J.Y.Lee, C.Chang, H.K.Song, J.Moon, J.K.Yang, H.K.Kim, S.T.Kwon, and S.W.Suh (2000).
Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.
  EMBO J, 19, 1119-1129.
PDB codes: 1dgs 1dgt 1v9p
11095673 M.A.Petit, and S.D.Ehrlich (2000).
The NAD-dependent ligase encoded by yerG is an essential gene of Bacillus subtilis.
  Nucleic Acids Res, 28, 4642-4648.  
11106756 M.Odell, V.Sriskanda, S.Shuman, and D.B.Nikolov (2000).
Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.
  Mol Cell, 6, 1183-1193.
PDB code: 1fvi
10871342 V.Sriskanda, Z.Kelman, J.Hurwitz, and S.Shuman (2000).
Characterization of an ATP-dependent DNA ligase from the thermophilic archaeon Methanobacterium thermoautotrophicum.
  Nucleic Acids Res, 28, 2221-2228.  
10508675 A.E.Todd, C.A.Orengo, and J.M.Thornton (1999).
Evolution of protein function, from a structural perspective.
  Curr Opin Chem Biol, 3, 548-556.  
  10543760 G.Ciarrocchi, D.G.MacPhee, L.W.Deady, and L.Tilley (1999).
Specific inhibition of the eubacterial DNA ligase by arylamino compounds.
  Antimicrob Agents Chemother, 43, 2766-2772.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.