PDBsum entry 1in1

Go to PDB code: 
protein links
Ligase PDB id
Jmol PyMol
Protein chain
88 a.a. *
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Nmr structure of human DNA ligase iiialpha brct domain
Structure: DNA ligase iii. Chain: a. Fragment: brct domain. Synonym: polydeoxyribonucleotide synthase [atp]. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: V.V.Krishnan,K.H.Thornton,M.P.Thelen,M.Cosman
Key ref:
V.V.Krishnan et al. (2001). Solution structure and backbone dynamics of the human DNA ligase IIIalpha BRCT domain. Biochemistry, 40, 13158-13166. PubMed id: 11683624 DOI: 10.1021/bi010979g
11-May-01     Release date:   25-May-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P49916  (DNLI3_HUMAN) -  DNA ligase 3
1009 a.a.
88 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Dna ligase (ATP).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate
+ (deoxyribonucleotide)(n)-3'-hydroxyl
+ 5'-phospho- (deoxyribonucleotide)(m)
= (deoxyribonucleotide)(n+m)
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site


DOI no: 10.1021/bi010979g Biochemistry 40:13158-13166 (2001)
PubMed id: 11683624  
Solution structure and backbone dynamics of the human DNA ligase IIIalpha BRCT domain.
V.V.Krishnan, K.H.Thornton, M.P.Thelen, M.Cosman.
BRCT (BRCA1 carboxyl terminus) domains are found in a number of DNA repair enzymes and cell cycle regulators and are believed to mediate important protein-protein interactions. The DNA ligase IIIalpha BRCT domain partners with the distal BRCT domain of the DNA repair protein XRCC1 (X1BRCTb) in the DNA base excision repair (BER) pathway. To elucidate the mechanisms by which these two domains can interact, we have determined the solution structure of human ligase IIIalpha BRCT (L3[86], residues 837-922). The structure of L3[86] consists of a beta2beta1beta3beta4 parallel sheet with a two-alpha-helix bundle packed against one face of the sheet. This fold is conserved in several proteins having a wide range of activities, including X1BRCTb [Zhang, X. D., et al. (1998) EMBO J. 17, 6404-6411]. L3[86] exists as a dimer in solution, but an insufficient number of NOE restraints precluded the determination of the homodimer structure. However, 13C isotope-filtered and hydrogen-deuterium exchange experiments indicate that the N-terminus, alpha1, the alpha1-beta2 loop, and the three residues following alpha2 are involved in forming the dimer interface, as similarly observed in the structure of X1BRCTb. NOE and dynamic data indicate that several residues (837-844) in the N-terminal region appear to interconvert between helix and random coil conformations. Further studies of other BRCT domains and of their complexes are needed to address how these proteins interact with one another, and to shed light on how mutations can lead to disruption of function and ultimately disease.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20724438 M.Rappas, A.W.Oliver, and L.H.Pearl (2011).
Structure and function of the Rad9-binding region of the DNA-damage checkpoint adaptor TopBP1.
  Nucleic Acids Res, 39, 313-324.
PDB codes: 2xnh 2xnk
19502749 Y.Mizushina (2009).
Specific inhibitors of mammalian DNA polymerase species.
  Biosci Biotechnol Biochem, 73, 1239-1251.  
18579587 A.Kumar, W.S.Joo, G.Meinke, S.Moine, E.N.Naumova, and P.A.Bullock (2008).
Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses.
  J Virol, 82, 8849-8862.  
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.  
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.  
17915942 E.F.DeRose, M.W.Clarkson, S.A.Gilmore, C.J.Galban, A.Tripathy, J.M.Havener, G.A.Mueller, D.A.Ramsden, R.E.London, and A.L.Lee (2007).
Solution structure of polymerase mu's BRCT Domain reveals an element essential for its role in nonhomologous end joining.
  Biochemistry, 46, 12100-12110.
PDB code: 2htf
17094803 D.C.Zappulla, A.S.Maharaj, J.J.Connelly, R.A.Jockusch, and R.Sternglanz (2006).
Rtt107/Esc4 binds silent chromatin and DNA repair proteins using different BRCT motifs.
  BMC Mol Biol, 7, 40.  
16807234 M.K.El-Tanani, F.C.Campbell, P.Crowe, P.Erwin, D.P.Harkin, P.Pharoah, B.Ponder, and P.S.Rudland (2006).
BRCA1 suppresses osteopontin-mediated breast cancer.
  J Biol Chem, 281, 26587-26601.  
16361700 M.Kobayashi, F.Figaroa, N.Meeuwenoord, L.E.Jansen, and G.Siegal (2006).
Characterization of the DNA binding and structural properties of the BRCT region of human replication factor C p140 subunit.
  J Biol Chem, 281, 4308-4317.  
16648486 N.Puebla-Osorio, D.B.Lacey, F.W.Alt, and C.Zhu (2006).
Early embryonic lethality due to targeted inactivation of DNA ligase III.
  Mol Cell Biol, 26, 3935-3941.  
16483311 T.Takeuchi, T.Ishidoh, H.Iijima, I.Kuriyama, N.Shimazaki, O.Koiwai, K.Kuramochi, S.Kobayashi, F.Sugawara, K.Sakaguchi, H.Yoshida, and Y.Mizushina (2006).
Structural relationship of curcumin derivatives binding to the BRCT domain of human DNA polymerase lambda.
  Genes Cells, 11, 223-235.  
15987676 P.T.Beernink, M.Hwang, M.Ramirez, M.B.Murphy, S.A.Doyle, and M.P.Thelen (2005).
Specificity of protein interactions mediated by BRCT domains of the XRCC1 DNA repair protein.
  J Biol Chem, 280, 30206-30213.  
15501676 J.N.Glover, R.S.Williams, and M.S.Lee (2004).
Interactions between BRCT repeats and phosphoproteins: tangled up in two.
  Trends Biochem Sci, 29, 579-585.  
15133503 R.S.Williams, M.S.Lee, D.D.Hau, and J.N.Glover (2004).
Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1.
  Nat Struct Mol Biol, 11, 519-525.
PDB codes: 1t2u 1t2v
14578343 M.Rodriguez, X.Yu, J.Chen, and Z.Songyang (2003).
Phosphopeptide binding specificities of BRCA1 COOH-terminal (BRCT) domains.
  J Biol Chem, 278, 52914-52918.  
12427738 R.S.Williams, and J.N.Glover (2003).
Structural consequences of a cancer-causing BRCA1-BRCT missense mutation.
  J Biol Chem, 278, 2630-2635.
PDB code: 1n5o
12110597 D.J.Derbyshire, B.P.Basu, L.C.Serpell, W.S.Joo, T.Date, K.Iwabuchi, and A.J.Doherty (2002).
Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor.
  EMBO J, 21, 3863-3872.
PDB code: 1gzh
12351827 D.J.Derbyshire, B.P.Basu, T.Date, K.Iwabuchi, and A.J.Doherty (2002).
Purification, crystallization and preliminary X-ray analysis of the BRCT domains of human 53BP1 bound to the p53 tumour suppressor.
  Acta Crystallogr D Biol Crystallogr, 58, 1826-1829.  
  11983065 I.V.Martin, and S.A.MacNeill (2002).
ATP-dependent DNA ligases.
  Genome Biol, 3, REVIEWS3005.  
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 codes are shown on the right.