PDBsum entry 1uw0

Go to PDB code: 
protein metals links
Ligase PDB id
Protein chain
117 a.a. *
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Solution structure of the zinc-finger domain from DNA ligase iiia
Structure: DNA ligase iii. Chain: a. Fragment: zinc-finger domain, residues 1-117. Synonym: polydeoxyribonucleotide synthase [atp]. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: codon plus rp.
NMR struc: 28 models
Authors: A.W.Kulczyk,J.-C.Yang,D.Neuhaus
Key ref:
A.W.Kulczyk et al. (2004). Solution structure and DNA binding of the zinc-finger domain from DNA ligase IIIalpha. J Mol Biol, 341, 723-738. PubMed id: 15288782 DOI: 10.1016/j.jmb.2004.06.035
27-Jan-04     Release date:   05-Aug-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P49916  (DNLI3_HUMAN) -  DNA ligase 3
1009 a.a.
117 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Dna ligase (ATP).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m)
+ (deoxyribonucleotide)(n)
+ (deoxyribonucleotide)(m)
+ diphosphate
+ (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 binding     2 terms  


DOI no: 10.1016/j.jmb.2004.06.035 J Mol Biol 341:723-738 (2004)
PubMed id: 15288782  
Solution structure and DNA binding of the zinc-finger domain from DNA ligase IIIalpha.
A.W.Kulczyk, J.C.Yang, D.Neuhaus.
DNA ligase IIIalpha carries out the final ligation step in the base excision repair (BER) and single strand break repair (SSBR) mechanisms of DNA repair. The enzyme recognises single-strand nicks and other damage features in double-stranded DNA, both through the catalytic domain and an N-terminal domain containing a single zinc finger. The latter is homologous to other zinc fingers that recognise damaged DNA, two in the N terminus of poly(adenosine-ribose)polymerase and three in the N terminus of the Arabidopsis thaliana nick-sensing DNA 3'-phosphoesterase. Here, we present the solution structure of the zinc-finger domain of human DNA ligase IIIalpha, the first structure of a finger from this group. It is related to that of the erythroid transcription factor GATA-1, but has an additional N-terminal beta-strand and C-terminal alpha-helix. Chemical shift mapping using a DNA ligand containing a single-stranded break showed that the DNA-binding surface of the DNA-ligase IIIalpha zinc finger is substantially different from that of GATA-1, consistent with the fact that the two proteins recognise very different features in the DNA. Likely implications for DNA binding are discussed.
  Selected figure(s)  
Figure 1.
Figure 1. Multiple sequence alignment across all PARP-like fingers found in the NR database at NCBI, produced using the program T-COFFEE. Residues are coloured by type: red, positively charged; blue, negatively charged; cyan, hydrophobic; green, hydrophilic; yellow, Pro; grey, Gly. The zinc-binding residues are shown in magenta with a black triangle beneath. Sequence numbering is based on the human DL3a sequence. Sequence names are coded L3 for ligase III, P1 and P2, respectively, for fingers 1 and 2 of PARP, and A1, A2 and A3, respectively, for fingers 1, 2 and 3 of AtZDP.
Figure 5.
Figure 5. Histogram of 15N{1H} NOE enhancement ratios as a function of sequence.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 341, 723-738) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
18215166 S.Petrucco, and R.Percudani (2008).
Structural recognition of DNA by poly(ADP-ribose)polymerase-like zinc finger families.
  FEBS J, 275, 883-893.  
18518823 T.Ellenberger, and A.E.Tomkinson (2008).
Eukaryotic DNA ligases: structural and functional insights.
  Annu Rev Biochem, 77, 313-338.  
17503083 M.J.Roach, and M.K.Deyholos (2007).
Microarray analysis of flax (Linum usitatissimum L.) stems identifies transcripts enriched in fibre-bearing phloem tissues.
  Mol Genet Genomics, 278, 149-165.  
16425174 L.Grajcar, C.El Amri, M.Ghomi, S.Fermandjian, V.Huteau, R.Mandel, S.Lecomte, and M.H.Baron (2006).
Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy.
  Biopolymers, 82, 6.  
16855289 O.Mortusewicz, U.Rothbauer, M.C.Cardoso, and H.Leonhardt (2006).
Differential recruitment of DNA Ligase I and III to DNA repair sites.
  Nucleic Acids Res, 34, 3523-3532.  
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.