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PDBsum entry 1a0i

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protein ligands links
Ligase PDB id
1a0i
Jmol
Contents
Protein chain
332 a.a. *
Ligands
ATP
Waters ×193
* Residue conservation analysis
PDB id:
1a0i
Name: Ligase
Title: Atp-dependent DNA ligase from bacteriophage t7 complex with atp
Structure: DNA ligase. Chain: a. Engineered: yes. Mutation: yes
Source: Enterobacteria phage t7. Organism_taxid: 10760. Gene: lig. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.60Å     R-factor:   0.222     R-free:   0.341
Authors: H.S.Subramanya,A.J.Doherty,S.R.Ashford,D.B.Wigley
Key ref:
H.S.Subramanya et al. (1996). Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell, 85, 607-615. PubMed id: 8653795 DOI: 10.1016/S0092-8674(00)81260-X
Date:
01-Dec-97     Release date:   25-Mar-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00969  (DNLI_BPT7) -  DNA ligase
Seq:
Struc:
359 a.a.
332 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.6.5.1.1  - Dna ligase (ATP).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m)
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+ (deoxyribonucleotide)(n)
+ (deoxyribonucleotide)(m)
= AMP
+ diphosphate
+ (deoxyribonucleotide)(n+m)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to DNA damage stimulus   5 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(00)81260-X Cell 85:607-615 (1996)
PubMed id: 8653795  
 
 
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
H.S.Subramanya, A.J.Doherty, S.R.Ashford, D.B.Wigley.
 
  ABSTRACT  
 
The crystal structure of the ATP-dependent DNA ligase from bacteriophage T7 has been solved at 2.6 A resolution. The protein comprises two domains with a deep cleft running between them. The structure of a complex with ATP reveals that the nucleotide binding pocket is situated on the larger N-terminal domain, at the base of the cleft between the two domains of the enzyme. Comparison of the overall domain structure with that of DNA methyltransferases, coupled with other evidence, suggests that DNA also binds in this cleft. Since this structure is the first of the nucleotidyltransferase superfamily, which includes the eukaryotic mRNA capping enzymes, the relationship between the structure of DNA ligase and that of other nucleotidyltransferases is also discussed.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Ribbon Diagram Illustrating the Domain Structure of the ProteinThe N-terminal domain (domain 1) is colored in green and the C-terminal domain (domain 2) in red. The bound ATP is overlaid in blue. This figure was prepared using the program RIBBONS ([5]).
Figure 6.
Figure 6. Proposed General Mechanism for Ligases and Related Nucleotidyltransferases
 
  The above figures are reprinted by permission from Cell Press: Cell (1996, 85, 607-615) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21146395 E.S.Kim, B.J.Hong, C.W.Park, Y.Kim, J.W.Park, and K.Y.Choi (2011).
Effects of lateral spacing on enzymatic on-chip DNA polymerization.
  Biosens Bioelectron, 26, 2566-2573.  
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.  
19854942 J.Kim, and M.Mrksich (2010).
Profiling the selectivity of DNA ligases in an array format with mass spectrometry.
  Nucleic Acids Res, 38, e2.  
  21129204 T.C.Mueser, J.M.Hinerman, J.M.Devos, R.A.Boyer, and K.J.Williams (2010).
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.
  Virol J, 7, 359.  
19255439 K.Mayanagi, S.Kiyonari, M.Saito, T.Shirai, Y.Ishino, and K.Morikawa (2009).
Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture.
  Proc Natl Acad Sci U S A, 106, 4647-4652.  
20354588 R.V.Swift, and R.E.Amaro (2009).
Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms.
  Expert Opin Drug Discov, 4, 1281-1294.  
19329793 S.Shuman (2009).
DNA ligases: progress and prospects.
  J Biol Chem, 284, 17365-17369.  
20636060 T.Conze, A.Shetye, Y.Tanaka, J.Gu, C.Larsson, J.Göransson, G.Tavoosidana, O.Söderberg, M.Nilsson, and U.Landegren (2009).
Analysis of genes, transcripts, and proteins via DNA ligation.
  Annu Rev Anal Chem (Palo Alto Calif), 2, 215-239.  
18562298 A.V.Cherepanov, E.V.Doroshenko, J.Matysik, S.de Vries, and H.J.de Groot (2008).
The associative nature of adenylyl transfer catalyzed by T4 DNA ligase.
  Proc Natl Acad Sci U S A, 105, 8563-8568.  
18238776 E.Cotner-Gohara, I.K.Kim, A.E.Tomkinson, and T.Ellenberger (2008).
Two DNA-binding and nick recognition modules in human DNA ligase III.
  J Biol Chem, 283, 10764-10772.  
18262407 J.M.Pascal (2008).
DNA and RNA ligases: structural variations and shared mechanisms.
  Curr Opin Struct Biol, 18, 96.  
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.  
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
17618295 P.A.Nair, J.Nandakumar, P.Smith, M.Odell, C.D.Lima, and S.Shuman (2007).
Structural basis for nick recognition by a minimal pluripotent DNA ligase.
  Nat Struct Mol Biol, 14, 770-778.
PDB codes: 2q2t 2q2u
17506672 R.S.Pitcher, N.C.Brissett, and A.J.Doherty (2007).
Nonhomologous end-joining in bacteria: a microbial perspective.
  Annu Rev Microbiol, 61, 259-282.  
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.  
16420348 A.Zhao, F.C.Gray, and S.A.MacNeill (2006).
ATP- and NAD+-dependent DNA ligases share an essential function in the halophilic archaeon Haloferax volcanii.
  Mol Microbiol, 59, 743-752.  
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
17052461 J.M.Pascal, O.V.Tsodikov, G.L.Hura, W.Song, E.A.Cotner, S.Classen, A.E.Tomkinson, J.A.Tainer, and T.Ellenberger (2006).
A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA.
  Mol Cell, 24, 279-291.
PDB codes: 2hii 2hik 2hiv 2hix
17068206 L.K.Wang, B.Schwer, and S.Shuman (2006).
Structure-guided mutational analysis of T4 RNA ligase 1.
  RNA, 12, 2126-2134.  
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
16614906 Y.J.Kim, H.S.Lee, S.S.Bae, J.H.Jeon, S.H.Yang, J.K.Lim, S.G.Kang, S.T.Kwon, and J.H.Lee (2006).
Cloning, expression, and characterization of a DNA ligase from a hyperthermophilic archaeon Thermococcus sp.
  Biotechnol Lett, 28, 401-407.  
15987807 A.Martins, and S.Shuman (2005).
An end-healing enzyme from Clostridium thermocellum with 5' kinase, 2',3' phosphatase, and adenylyltransferase activities.
  RNA, 11, 1271-1280.  
15920472 A.Strasser, A.Dickmanns, R.Lührmann, and R.Ficner (2005).
Structural basis for m3G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1.
  EMBO J, 24, 2235-2243.
PDB code: 1xk5
15520014 H.Zhu, and S.Shuman (2005).
A primer-dependent polymerase function of pseudomonas aeruginosa ATP-dependent DNA ligase (LigD).
  J Biol Chem, 280, 418-427.  
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.  
15767682 J.A.Law, C.E.Huang, S.F.O'Hearn, and B.Sollner-Webb (2005).
In Trypanosoma brucei RNA editing, band II enables recognition specifically at each step of the U insertion cycle.
  Mol Cell Biol, 25, 2785-2794.  
15923379 L.K.Wang, and S.Shuman (2005).
Structure-function analysis of yeast tRNA ligase.
  RNA, 11, 966-975.  
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.  
16199559 N.Keppetipola, and S.Shuman (2005).
Characterization of a thermophilic ATP-dependent DNA ligase from the euryarchaeon Pyrococcus horikoshii.
  J Bacteriol, 187, 6902-6908.  
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.  
14747466 A.Martins, and S.Shuman (2004).
Characterization of a baculovirus enzyme with RNA ligase, polynucleotide 5'-kinase, and polynucleotide 3'-phosphatase activities.
  J Biol Chem, 279, 18220-18231.  
15333634 A.Martins, and S.Shuman (2004).
An RNA ligase from Deinococcus radiodurans.
  J Biol Chem, 279, 50654-50661.  
14985346 C.Gong, A.Martins, P.Bongiorno, M.Glickman, and S.Shuman (2004).
Biochemical and genetic analysis of the four DNA ligases of mycobacteria.
  J Biol Chem, 279, 20594-20606.  
14962393 C.K.Ho, L.K.Wang, C.D.Lima, and S.Shuman (2004).
Structure and mechanism of RNA ligase.
  Structure, 12, 327-339.
PDB code: 1s68
15056675 H.Zhu, S.Yin, and S.Shuman (2004).
Characterization of polynucleotide kinase/phosphatase enzymes from Mycobacteriophages omega and Cjw1 and vibriophage KVP40.
  J Biol Chem, 279, 26358-26369.  
15037606 I.Bougie, and M.Bisaillon (2004).
The broad spectrum antiviral nucleoside ribavirin as a substrate for a viral RNA capping enzyme.
  J Biol Chem, 279, 22124-22130.  
14752051 I.V.Martin, and S.A.MacNeill (2004).
Functional analysis of subcellular localization and protein-protein interaction sequences in the essential DNA ligase I protein of fission yeast.
  Nucleic Acids Res, 32, 632-642.  
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
15084599 J.Nandakumar, C.K.Ho, C.D.Lima, and S.Shuman (2004).
RNA substrate specificity and structure-guided mutational analysis of bacteriophage T4 RNA ligase 2.
  J Biol Chem, 279, 31337-31347.  
15494308 J.Nandakumar, and S.Shuman (2004).
How an RNA ligase discriminates RNA versus DNA damage.
  Mol Cell, 16, 211-221.  
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.  
14536071 A.Schnaufer, N.L.Ernst, S.S.Palazzo, J.O'Rear, R.Salavati, and K.Stuart (2003).
Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex.
  Mol Cell, 12, 307-319.  
12820968 C.Fabrega, V.Shen, S.Shuman, and C.D.Lima (2003).
Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II.
  Mol Cell, 11, 1549-1561.
PDB code: 1p16
14602897 E.A.Worthey, A.Schnaufer, I.S.Mian, K.Stuart, and R.Salavati (2003).
Comparative analysis of editosome proteins in trypanosomatids.
  Nucleic Acids Res, 31, 6392-6408.  
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.  
12766156 L.K.Wang, C.K.Ho, Y.Pei, and S.Shuman (2003).
Mutational analysis of bacteriophage T4 RNA ligase 1. Different functional groups are required for the nucleotidyl transfer and phosphodiester bond formation steps of the ligation reaction.
  J Biol Chem, 278, 29454-29462.  
12930960 M.Odell, L.Malinina, V.Sriskanda, M.Teplova, and S.Shuman (2003).
Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate.
  Nucleic Acids Res, 31, 5090-5100.
PDB code: 1p8l
12646557 P.Fechter, L.Mingay, J.Sharps, A.Chambers, E.Fodor, and G.G.Brownlee (2003).
Two aromatic residues in the PB2 subunit of influenza A RNA polymerase are crucial for cap binding.
  J Biol Chem, 278, 20381-20388.  
12933796 R.Sawaya, B.Schwer, and S.Shuman (2003).
Genetic and biochemical analysis of the functional domains of yeast tRNA ligase.
  J Biol Chem, 278, 43928-43938.  
12611899 S.Yin, C.K.Ho, and S.Shuman (2003).
Structure-function analysis of T4 RNA ligase 2.
  J Biol Chem, 278, 17601-17608.  
14654700 T.Blondal, S.H.Hjorleifsdottir, O.F.Fridjonsson, A.Aevarsson, S.Skirnisdottir, A.G.Hermannsdottir, G.O.Hreggvidsson, A.V.Smith, and J.K.Kristjansson (2003).
Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1.
  Nucleic Acids Res, 31, 7247-7254.  
12473094 A.V.Cherepanov, and S.de Vries (2002).
Dynamic mechanism of nick recognition by DNA ligase.
  Eur J Biochem, 269, 5993-5999.  
12228725 C.K.Ho, and S.Shuman (2002).
Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains.
  Proc Natl Acad Sci U S A, 99, 12709-12714.  
12445771 D.D.Boehr, A.R.Farley, G.D.Wright, and J.R.Cox (2002).
Analysis of the pi-pi stacking interactions between the aminoglycoside antibiotic kinase APH(3')-IIIa and its nucleotide ligands.
  Chem Biol, 9, 1209-1217.  
  11983065 I.V.Martin, and S.A.MacNeill (2002).
ATP-dependent DNA ligases.
  Genome Biol, 3, REVIEWS3005.  
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.  
11842101 V.Sriskanda, and S.Shuman (2002).
Role of nucleotidyltransferase motifs I, III and IV in the catalysis of phosphodiester bond formation by Chlorella virus DNA ligase.
  Nucleic Acids Res, 30, 903-911.  
11721015 A.V.Cherepanov, and S.de Vries (2001).
Binding of nucleotides by T4 DNA ligase and T4 RNA ligase: optical absorbance and fluorescence studies.
  Biophys J, 81, 3545-3559.  
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.  
11167066 J.Banér, M.Nilsson, A.Isaksson, M.Mendel-Hartvig, D.O.Antson, and U.Landegren (2001).
More keys to padlock probes: mechanisms for high-throughput nucleic acid analysis.
  Curr Opin Biotechnol, 12, 11-15.  
11157762 S.Kawaguchi, J.Müller, D.Linde, S.Kuramitsu, T.Shibata, Y.Inoue, D.G.Vassylyev, and S.Yokoyama (2001).
The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus.
  EMBO J, 20, 562-569.
PDB code: 1gd7
12762032 S.Shuman (2001).
The mRNA capping apparatus as drug target and guide to eukaryotic phylogeny.
  Cold Spring Harb Symp Quant Biol, 66, 301-312.  
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.  
10644745 C.L.Luongo, K.M.Reinisch, S.C.Harrison, and M.L.Nibert (2000).
Identification of the guanylyltransferase region and active site in reovirus mRNA capping protein lambda2.
  J Biol Chem, 275, 2804-2810.  
10637340 J.N.Housby, S.H.Thorbjarnardóttir, Z.O.Jónsson, and E.M.Southern (2000).
Optimised ligation of oligonucleotides by thermal ligases: comparison of Thermus scotoductus and Rhodothermus marinus DNA ligases to other thermophilic ligases.
  Nucleic Acids Res, 28, E10.  
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
10713526 J.Y.Lee, H.K.Kim, C.Chang, S.H.Eom, K.Y.Hwang, Y.Cho, Y.G.Yu, S.E.Ryu, S.T.Kwon, and S.W.Suh (2000).
Crystallization and preliminary x-ray crystallographic analysis of NAD+-dependent DNA ligase from Thermus filiformis.
  Acta Crystallogr D Biol Crystallogr, 56, 357-358.  
11053387 M.Nakatani, S.Ezaki, H.Atomi, and T.Imanaka (2000).
A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity.
  J Bacteriol, 182, 6424-6433.  
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
10982876 R.M.Taylor, C.J.Whitehouse, and K.W.Caldecott (2000).
The DNA ligase III zinc finger stimulates binding to DNA secondary structure and promotes end joining.
  Nucleic Acids Res, 28, 3558-3563.  
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.  
10085093 A.Arabshahi, and P.A.Frey (1999).
Standard free energy for the hydrolysis of adenylylated T4 DNA ligase and the apparent pKa of lysine 159.
  J Biol Chem, 274, 8586-8588.  
10589681 C.D.Lima, L.K.Wang, and S.Shuman (1999).
Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus.
  Cell, 99, 533-543.
PDB codes: 1d8h 1d8i
10395545 E.Riballo, S.E.Critchlow, S.H.Teo, A.J.Doherty, A.Priestley, B.Broughton, B.Kysela, H.Beamish, N.Plowman, C.F.Arlett, A.R.Lehmann, S.P.Jackson, and P.A.Jeggo (1999).
Identification of a defect in DNA ligase IV in a radiosensitive leukaemia patient.
  Curr Biol, 9, 699-702.  
  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.  
10318816 M.Odell, and S.Shuman (1999).
Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA.
  J Biol Chem, 274, 14032-14039.  
10368271 M.R.Singleton, K.Håkansson, D.J.Timson, and D.B.Wigley (1999).
Structure of the adenylation domain of an NAD+-dependent DNA ligase.
  Structure, 7, 35-42.
PDB code: 1b04
10047578 S.S.Parikh, C.D.Mol, D.J.Hosfield, and J.A.Tainer (1999).
Envisioning the molecular choreography of DNA base excision repair.
  Curr Opin Struct Biol, 9, 37-47.  
10419478 Z.B.Mackey, C.Niedergang, J.M.Murcia, J.Leppard, K.Au, J.Chen, G.de Murcia, and A.E.Tomkinson (1999).
DNA ligase III is recruited to DNA strand breaks by a zinc finger motif homologous to that of poly(ADP-ribose) polymerase. Identification of two functionally distinct DNA binding regions within DNA ligase III.
  J Biol Chem, 274, 21679-21687.  
9525883 D.F.Bogenhagen, and K.G.Pinz (1998).
The action of DNA ligase at abasic sites in DNA.
  J Biol Chem, 273, 7888-7893.  
9493270 J.L.Kim, K.A.Morgenstern, J.P.Griffith, M.D.Dwyer, J.A.Thomson, M.A.Murcko, C.Lin, and P.R.Caron (1998).
Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding.
  Structure, 6, 89.
PDB code: 1a1v
9722647 J.N.Housby, and E.M.Southern (1998).
Fidelity of DNA ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides.
  Nucleic Acids Res, 26, 4259-4266.  
9465045 K.Hâkansson, and D.B.Wigley (1998).
Structure of a complex between a cap analogue and mRNA guanylyl transferase demonstrates the structural chemistry of RNA capping.
  Proc Natl Acad Sci U S A, 95, 1505-1510.
PDB code: 1cko
9759487 R.J.Roberts, and X.Cheng (1998).
Base flipping.
  Annu Rev Biochem, 67, 181-198.  
9512541 T.Yamada-Okabe, R.Doi, O.Shimmi, M.Arisawa, and H.Yamada-Okabe (1998).
Isolation and characterization of a human cDNA for mRNA 5'-capping enzyme.
  Nucleic Acids Res, 26, 1700-1706.  
9421510 V.Sriskanda, and S.Shuman (1998).
Chlorella virus DNA ligase: nick recognition and mutational analysis.
  Nucleic Acids Res, 26, 525-531.  
9671815 V.Sriskanda, and S.Shuman (1998).
Specificity and fidelity of strand joining by Chlorella virus DNA ligase.
  Nucleic Acids Res, 26, 3536-3541.  
9363683 A.E.Tomkinson, and D.S.Levin (1997).
Mammalian DNA ligases.
  Bioessays, 19, 893-901.  
9060431 C.Cheng, and S.Shuman (1997).
Characterization of an ATP-dependent DNA ligase encoded by Haemophilus influenzae.
  Nucleic Acids Res, 25, 1369-1374.  
9254695 C.E.Pritchard, and E.M.Southern (1997).
Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases.
  Nucleic Acids Res, 25, 3403-3407.  
  9032324 C.K.Ho, J.L.Van Etten, and S.Shuman (1997).
Characterization of an ATP-dependent DNA ligase encoded by Chlorella virus PBCV-1.
  J Virol, 71, 1931-1937.  
9261078 G.Varani (1997).
A cap for all occasions.
  Structure, 5, 855-858.  
9016621 J.Sekiguchi, and S.Shuman (1997).
Domain structure of vaccinia DNA ligase.
  Nucleic Acids Res, 25, 727-734.  
  9371633 J.Sekiguchi, and S.Shuman (1997).
Nick sensing by vaccinia virus DNA ligase requires a 5' phosphate at the nick and occupancy of the adenylate binding site on the enzyme.
  J Virol, 71, 9679-9684.  
9160746 K.Håkansson, A.J.Doherty, S.Shuman, and D.B.Wigley (1997).
X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes.
  Cell, 89, 545-553.
PDB codes: 1ckm 1ckn
9008164 M.Bycroft, T.J.Hubbard, M.Proctor, S.M.Freund, and A.G.Murzin (1997).
The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.
  Cell, 88, 235-242.
PDB code: 1sro
  9271115 P.Schär, G.Herrmann, G.Daly, and T.Lindahl (1997).
A newly identified DNA ligase of Saccharomyces cerevisiae involved in RAD52-independent repair of DNA double-strand breaks.
  Genes Dev, 11, 1912-1924.  
9153309 R.Rossi, A.Montecucco, G.Ciarrocchi, and G.Biamonti (1997).
Functional characterization of the T4 DNA ligase: a new insight into the mechanism of action.
  Nucleic Acids Res, 25, 2106-2113.  
9275164 S.P.Wang, L.Deng, C.K.Ho, and S.Shuman (1997).
Phylogeny of mRNA capping enzymes.
  Proc Natl Acad Sci U S A, 94, 9573-9578.  
9111070 V.J.Mackenney, D.E.Barnes, and T.Lindahl (1997).
Specific function of DNA ligase I in simian virus 40 DNA replication by human cell-free extracts is mediated by the amino-terminal non-catalytic domain.
  J Biol Chem, 272, 11550-11556.  
8798671 P.Robins, and T.Lindahl (1996).
DNA ligase IV from HeLa cell nuclei.
  J Biol Chem, 271, 24257-24261.  
8805556 S.Shuman (1996).
Closing the gap on DNA ligase.
  Structure, 4, 653-656.  
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.