PDBsum entry 3ey1

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protein dna_rna ligands links
Hydrolase/DNA PDB id
Protein chain
137 a.a. *
GOL ×3
Waters ×103
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: A conformational transition in the structure of a 2'-thiomet modified DNA visualized at high resolution
Structure: Ribonuclease h. Chain: a. Fragment: rnase h domain, unp residues 59-196. Synonym: rnase h. Engineered: yes. Mutation: yes. 5'-d( Cp Gp Cp Gp Ap Ap (Usm)p (Usm)p Cp Gp Cp G) chain: b. Engineered: yes.
Source: Bacillus halodurans. Organism_taxid: 86665. Gene: rnha, bh0863. Synthetic: yes. Other_details: chemically synthesized modified dodecamer dn (oligonucleotide)
1.60Å     R-factor:   0.193     R-free:   0.261
Authors: M.Egli,P.S.Pallan
Key ref: P.S.Pallan et al. (2009). A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution. Chem Commun (Camb), 0, 2017-2019. PubMed id: 19333476
17-Oct-08     Release date:   28-Apr-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9KEI9  (RNH1_BACHD) -  Ribonuclease H
196 a.a.
137 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.  - Ribonuclease H.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     2 terms  


Chem Commun (Camb) 0:2017-2019 (2009)
PubMed id: 19333476  
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
P.S.Pallan, T.P.Prakash, F.Li, R.L.Eoff, M.Manoharan, M.Egli.
Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21340056 N.Erande, A.D.Gunjal, M.Fernandes, and V.A.Kumar (2011).
Probing the furanose conformation in the 2'-5'strand of isoDNA : RNA duplexes by freezing the nucleoside conformations.
  Chem Commun (Camb), 47, 4007-4009.  
20087997 M.Egli, and P.S.Pallan (2010).
Crystallographic studies of chemically modified nucleic acids: a backward glance.
  Chem Biodivers, 7, 60-89.  
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