PDBsum entry 2j6v

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
Protein chains
282 a.a. *
PO4 ×2
_MN ×6
Waters ×356
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of the DNA repair enzyme uv damage endonuclease
Structure: Uv endonuclease. Chain: a, b. Synonym: uvde. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 511693.
1.55Å     R-factor:   0.184     R-free:   0.212
Authors: K.Paspaleva,E.A.J.Thomassen,N.S.Pannu,N.Goossen, J.P.Abrahams
Key ref:
K.Paspaleva et al. (2007). Crystal structure of the DNA repair enzyme ultraviolet damage endonuclease. Structure, 15, 1316-1324. PubMed id: 17937920 DOI: 10.1016/j.str.2007.05.010
04-Oct-06     Release date:   16-Oct-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q746K1  (Q746K1_THET2) -  Probable UV endonuclease
280 a.a.
282 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     metal ion binding     2 terms  


DOI no: 10.1016/j.str.2007.05.010 Structure 15:1316-1324 (2007)
PubMed id: 17937920  
Crystal structure of the DNA repair enzyme ultraviolet damage endonuclease.
K.Paspaleva, E.Thomassen, N.S.Pannu, S.Iwai, G.F.Moolenaar, N.Goosen, J.P.Abrahams.
The ultraviolet damage endonuclease (UVDE) performs the initial step in an alternative excision repair pathway of UV-induced DNA damage, nicking immediately adjacent to the 5' phosphate of the damaged nucleotides. Unique for a single-protein DNA repair endonuclease, it can detect different types of damage. Here we show that Thermus thermophilus UVDE shares some essential structural features with Endo IV, an enzyme from the base excision repair pathway that exclusively nicks at abasic sites. A comparison between the structures indicates how DNA is bound by UVDE, how UVDE may recognize damage, and which of its residues are involved in catalysis. Furthermore, the comparison suggests an elegant explanation of UVDE's potential to recognize different types of damage. Incision assays including point mutants of UVDE confirmed the relevance of these conclusions.
  Selected figure(s)  
Figure 1.
Figure 1. UVDE Secondary Structure
View of the UVDE overall fold and topology. The α helices and β strands are labeled according to the canonical TIM-barrel fold and colored light blue and purple, respectively. The metal ions are colored blue with the coordinating phosphate in red.
Figure 2.
Figure 2. Metal Coordination
(A) The octahedrally coordinated metal ion is colored blue. The four coordinating residues, H231, D200, E269, and E175, are shown in ball-and-stick representation and colored orange. The phosphate coordinated by two oxygen atoms is colored red.
(B) The distorted bipyramidal coordination of the second metal ion by His-101, His-143, and Glu-175 and two oxygen atoms from the phosphate ion, while the third metal ion has an irregular four-fold coordination by one oxygen atom from the phosphate, His-244, His-203, and one water molecule. The residues involved in the coordination are colored light blue (H101, H143, H244, and H203). The phosphate is colored red, the water molecule is in green, and the metal ions are colored blue.
  The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 1316-1324) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21393072 K.Wagner, G.F.Moolenaar, and N.Goosen (2011).
Role of the insertion domain and the zinc-finger motif of Escherichia coli UvrA in damage recognition and ATP hydrolysis.
  DNA Repair (Amst), 10, 483-496.  
20386912 X.Chang, L.Yang, Q.Zhao, W.Fu, H.Chen, Z.Qiu, J.A.Chen, R.Hu, and W.Shu (2010).
Involvement of recF in 254 nm ultraviolet radiation resistance in Deinococcus radiodurans and Escherichia coli.
  Curr Microbiol, 61, 458-464.  
19241382 E.M.Meulenbroek, K.Paspaleva, E.A.Thomassen, J.P.Abrahams, N.Goosen, and N.S.Pannu (2009).
Involvement of a carboxylated lysine in UV damage endonuclease.
  Protein Sci, 18, 549-558.
PDB codes: 3bzg 3bzj 3c0l 3c0q 3c0s
19190661 O.D.Schärer, and A.J.Campbell (2009).
Wedging out DNA damage.
  Nat Struct Mol Biol, 16, 102-104.  
18408731 E.D.Garcin, D.J.Hosfield, S.A.Desai, B.J.Haas, M.Björas, R.P.Cunningham, and J.A.Tainer (2008).
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
  Nat Struct Mol Biol, 15, 515-522.
PDB codes: 2nq9 2nqh 2nqj
17937906 C.Kisker (2007).
When one protein does the job of many.
  Structure, 15, 1163-1165.  
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.