PDBsum entry 2d07

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protein Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
215 a.a. *
76 a.a. *
Waters ×104
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of sumo-3-modified thymine-DNA glycosylase
Structure: G/t mismatch-specific thymine DNA glycosylase. Chain: a. Fragment: central region. Synonym: tdg. Engineered: yes. Ubiquitin-like protein smt3b. Chain: b. Synonym: sentrin-2, ubiquitin-related protein sumo-3, hsmt3.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.10Å     R-factor:   0.208     R-free:   0.241
Authors: D.Baba,N.Maita,J.G.Jee,Y.Uchimura,H.Saitoh,K.Sugasawa, F.Hanaoka,H.Tochio,H.Hiroaki,M.Shirakawa
Key ref:
D.Baba et al. (2006). Crystal structure of SUMO-3-modified thymine-DNA glycosylase. J Mol Biol, 359, 137-147. PubMed id: 16626738 DOI: 10.1016/j.jmb.2006.03.036
26-Jul-05     Release date:   06-Jun-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q13569  (TDG_HUMAN) -  G/T mismatch-specific thymine DNA glycosylase
410 a.a.
215 a.a.
Protein chain
Pfam   ArchSchema ?
P61956  (SUMO2_HUMAN) -  Small ubiquitin-related modifier 2
95 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - Thymine-DNA glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   3 terms 
  Biological process     cellular protein metabolic process   7 terms 
  Biochemical function     protein binding     7 terms  


DOI no: 10.1016/j.jmb.2006.03.036 J Mol Biol 359:137-147 (2006)
PubMed id: 16626738  
Crystal structure of SUMO-3-modified thymine-DNA glycosylase.
D.Baba, N.Maita, J.G.Jee, Y.Uchimura, H.Saitoh, K.Sugasawa, F.Hanaoka, H.Tochio, H.Hiroaki, M.Shirakawa.
Modification of cellular proteins by the small ubiquitin-like modifier SUMO is important in regulating various cellular events. Many different nuclear proteins are targeted by SUMO, and the functional consequences of this modification are diverse. For most proteins, however, the functional and structural consequences of modification by specific SUMO isomers are unclear. Conjugation of SUMO to thymine-DNA glycosylase (TDG) induces the dissociation of TDG from its product DNA. Structure determination of the TDG central region conjugated to SUMO-1 previously suggested a mechanism in which the SUMOylation-induced conformational change in the C-terminal region of TDG releases TDG from tight binding to its product DNA. Here, we have determined the crystal structure of the central region of TDG conjugated to SUMO-3. The overall structure of SUMO-3-conjugated TDG is similar to the previously reported structure of TDG conjugated to SUMO-1, despite the relatively low level of amino acid sequence similarity between SUMO-3 and SUMO-1. The two structures revealed that the sequence of TDG that resembles the SUMO-binding motif (SBM) can form an intermolecular beta-sheet with either SUMO-1 or SUMO-3. Structural comparison with the canonical SBM shows that this SBM-like sequence of TDG retains all of the characteristic interactions of the SBM, indicating sequence diversity in the SBM.
  Selected figure(s)  
Figure 1.
Figure 1. Crystal structure of SUMO-3-TDG. (a) A presentation of the sequence and secondary structure of human TDG and SUMO-3. Residues present in the SUMO-3-TDG (the central region of TDG conjugated to SUMO-3) are shown in bold. Residues with electron density are shown in blue for TDG (the C-terminal segment, residues 301-330, in light-blue) and magenta for SUMO-3. (b) Stereo ribbon diagram of SUMO-3-TDG. The TDG core domain, TDG C-terminal segment, and SUMO-3 are shown in blue, light-blue, and magenta, respectively. Residues that lacked electron density (residues 200-202 of TDG, residues 91-93 of SUMO-3 and the isopeptide linkage) are shown as broken lines.
Figure 2.
Figure 2. Molecular interface between TDG and SUMO-3. (a) A stereo representation of molecular interface between TDG and SUMO-3. Residues from TDG and SUMO-3 are shown in blue and magenta, respectively. The missing isopeptide linkage between TDG and SUMO-3 is shown as a broken line. Stabilizing water molecules are in purple. (b) A diagram of the interactions between TDG and SUMO-3. Hydrophobic, hydrogen bond and electrostatic interactions are shown in green, blue and red, respectively. Protein residues are colored as in (a).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 137-147) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22382979 A.A.Armstrong, F.Mohideen, and C.D.Lima (2012).
Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2.
  Nature, 483, 59-63.
PDB codes: 3v60 3v61 3v62
21284855 C.Smet-Nocca, J.M.Wieruszeski, H.Léger, S.Eilebrecht, and A.Benecke (2011).
SUMO-1 regulates the conformational dynamics of Thymine-DNA Glycosylase regulatory domain and competes with its DNA binding activity.
  BMC Biochem, 12, 4.  
19236054 R.Kanagasabai, S.Liu, S.Salama, E.F.Yamasaki, L.Zhang, K.B.Greenchurch, and R.M.Snapka (2009).
Ubiquitin-family modifications of topoisomerase I in camptothecin-treated human breast cancer cells.
  Biochemistry, 48, 3176-3185.  
19339993 S.Y.Wu, and C.M.Chiang (2009).
Crosstalk between sumoylation and acetylation regulates p53-dependent chromatin transcription and DNA binding.
  EMBO J, 28, 1246-1259.  
18538649 F.Mohideen, and C.D.Lima (2008).
SUMO takes control of a ubiquitin-specific protease.
  Mol Cell, 30, 539-540.  
18451503 H.Hosono, and H.Yokosawa (2008).
Small ubiquitin-related modifier is secreted and shows cytokine-like activity.
  Biol Pharm Bull, 31, 834-837.  
18842587 N.Sekiyama, T.Ikegami, T.Yamane, M.Ikeguchi, Y.Uchimura, D.Baba, M.Ariyoshi, H.Tochio, H.Saitoh, and M.Shirakawa (2008).
Structure of the Small Ubiquitin-like Modifier (SUMO)-interacting Motif of MBD1-containing Chromatin-associated Factor 1 Bound to SUMO-3.
  J Biol Chem, 283, 35966-35975.  
17545995 O.Kerscher (2007).
SUMO junction-what's your function? New insights through SUMO-interacting motifs.
  EMBO Rep, 8, 550-555.  
17855402 X.Guan, A.Madabushi, D.Y.Chang, M.E.Fitzgerald, G.Shi, A.C.Drohat, and A.L.Lu (2007).
The human checkpoint sensor Rad9-Rad1-Hus1 interacts with and stimulates DNA repair enzyme TDG glycosylase.
  Nucleic Acids Res, 35, 6207-6218.  
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.