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PDBsum entry 1yua

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protein links
DNA binding protein PDB id
1yua
Jmol
Contents
Protein chain
122 a.a. *
* Residue conservation analysis
PDB id:
1yua
Name: DNA binding protein
Title: C-terminal domain of escherichia coli topoisomerase i
Structure: Topoisomerase i. Chain: a. Fragment: 122 c-terminal residues. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: dh5ai. Expressed in: escherichia coli. Expression_system_taxid: 562. Coli topoisomerase i
NMR struc: 26 models
Authors: L.Yu,C.-X.Zhu,Y.-C.Tse-Dinh,S.W.Fesik
Key ref:
L.Yu et al. (1995). Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I. Biochemistry, 34, 7622-7628. PubMed id: 7779808
Date:
02-Mar-95     Release date:   08-Mar-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06612  (TOP1_ECOLI) -  DNA topoisomerase 1
Seq:
Struc:
 
Seq:
Struc:
865 a.a.
122 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.5.99.1.2  - Dna topoisomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     chromosome   1 term 
  Biological process     DNA topological change   1 term 
  Biochemical function     DNA binding     2 terms  

 

 
Biochemistry 34:7622-7628 (1995)
PubMed id: 7779808  
 
 
Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I.
L.Yu, C.X.Zhu, Y.C.Tse-Dinh, S.W.Fesik.
 
  ABSTRACT  
 
Escherichia coli DNA topoisomerase I catalyzes the interconversion of different topological forms of DNA. In this paper we describe NMR studies of a 14K C-terminal fragment of this enzyme that binds preferentially to single-stranded DNA and enhances the enzyme's ability to relax negatively supercoiled DNA under high salt conditions. The 1H, 13C, and 15N resonances of the protein were assigned from a number of heteronuclear multidimensional NMR experiments, and the three-dimensional structure of the protein was determined from a total of 2188 NMR-derived restraints. The root-mean-square deviation about the mean coordinate positions for residues 13-120 is 0.68 +/- 0.11 A for the backbone atoms and 1.09 +/- 0.09 A for all heavy atoms. The overall fold, which consists of two four-stranded beta-sheets separated by two helices, differs from other DNA- and RNA-binding proteins such as gene 5, cold shock protein, and hnRNP C. From an analysis of the changes in chemical shift upon the addition of single-stranded DNA, the location of the oligonucleotide binding site was determined. The binding site consists of a beta-sheet containing positively charged and aromatic amino acids and, in spite of its different structure, is similar to that found in other proteins that bind single-stranded oligonucleotides.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19106140 N.M.Baker, R.Rajan, and A.Mondragón (2009).
Structural studies of type I topoisomerases.
  Nucleic Acids Res, 37, 693-701.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
16645812 L.Yu, P.J.Hajduk, J.Mack, and E.T.Olejniczak (2006).
Structural studies of Bcl-xL/ligand complexes using 19F NMR.
  J Biomol NMR, 34, 221-227.  
15537633 J.L.Plank, S.H.Chu, J.R.Pohlhaus, T.Wilson-Sali, and T.S.Hsieh (2005).
Drosophila melanogaster topoisomerase IIIalpha preferentially relaxes a positively or negatively supercoiled bubble substrate and is essential during development.
  J Biol Chem, 280, 3564-3573.  
16192570 Z.Li, H.Hiasa, and R.DiGate (2005).
Bacillus cereus DNA topoisomerase I and IIIalpha: purification, characterization and complementation of Escherichia coli TopoIII activity.
  Nucleic Acids Res, 33, 5415-5425.  
15139806 K.D.Corbett, and J.M.Berger (2004).
Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases.
  Annu Rev Biophys Biomol Struct, 33, 95.  
11809893 A.Das, C.Mandal, A.Dasgupta, T.Sengupta, and H.K.Majumder (2002).
An insight into the active site of a type I DNA topoisomerase from the kinetoplastid protozoan Leishmania donovani.
  Nucleic Acids Res, 30, 794-802.
PDB code: 1juw
11809772 K.Perry, and A.Mondragón (2002).
Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis.
  J Biol Chem, 277, 13237-13245.  
11395412 J.J.Champoux (2001).
DNA topoisomerases: structure, function, and mechanism.
  Annu Rev Biochem, 70, 369-413.  
10841763 M.R.Redinbo, J.J.Champoux, and W.G.Hol (2000).
Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA.
  Biochemistry, 39, 6832-6840.
PDB code: 1ej9
10047584 M.R.Redinbo, J.J.Champoux, and W.G.Hol (1999).
Structural insights into the function of type IB topoisomerases.
  Curr Opin Struct Biol, 9, 29-36.  
  10493576 M.Young, K.Kirshenbaum, K.A.Dill, and S.Highsmith (1999).
Predicting conformational switches in proteins.
  Protein Sci, 8, 1752-1764.  
10049334 T.C.Mou, C.W.Gray, and D.M.Gray (1999).
The binding affinity of Ff gene 5 protein depends on the nearest-neighbor composition of the ssDNA substrate.
  Biophys J, 76, 1537-1551.  
9748476 J.M.Berger (1998).
Structure of DNA topoisomerases.
  Biochim Biophys Acta, 1400, 3.  
9497321 S.J.Chen, and J.C.Wang (1998).
Identification of active site residues in Escherichia coli DNA topoisomerase I.
  J Biol Chem, 273, 6050-6056.  
9164449 D.Suck (1997).
Common fold, common function, common origin?
  Nat Struct Biol, 4, 161-165.  
9230044 R.H.Folmer, M.Nilges, C.H.Papavoine, B.J.Harmsen, R.N.Konings, and C.W.Hilbers (1997).
Refined structure, DNA binding studies, and dynamics of the bacteriophage Pf3 encoded single-stranded DNA binding protein.
  Biochemistry, 36, 9120-9135.  
8768898 A.J.Wand, and S.W.Englander (1996).
Protein complexes studied by NMR spectroscopy.
  Curr Opin Biotechnol, 7, 403-408.  
8621552 H.L.Zhang, S.Malpure, Z.Li, H.Hiasa, and R.J.DiGate (1996).
The role of the carboxyl-terminal amino acid residues in Escherichia coli DNA topoisomerase III-mediated catalysis.
  J Biol Chem, 271, 9039-9045.  
8703937 L.Yu, C.X.Zhu, Y.C.Tse-Dinh, and S.W.Fesik (1996).
Backbone dynamics of the C-terminal domain of Escherichia coli topoisomerase I in the absence and presence of single-stranded DNA.
  Biochemistry, 35, 9661-9666.  
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.