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PDBsum entry 1sxp

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protein dna_rna ligands links
Transferase/DNA PDB id
1sxp
Jmol
Contents
Protein chains
351 a.a.
DNA/RNA
Ligands
PG4
GOL ×3
Waters ×239
PDB id:
1sxp
Name: Transferase/DNA
Title: Bgt in complex with a 13mer DNA containing a central a:g mis
Structure: 5'-d( A Ap Tp Ap Cp Tp Ap Ap Gp Ap Tp Ap G)-3'. Chain: c. Engineered: yes. 5'-d( Cp Tp Ap Tp Cp Tp Gp Ap Gp Tp Ap Tp T)-3'. Chain: d. Engineered: yes. DNA beta-glucosyltransferase. Chain: a, b. Synonym: bgt.
Source: Synthetic: yes. Enterobacteria phage t4. Organism_taxid: 10665. Gene: bgt, beta-gt. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.212     R-free:   0.272
Authors: L.Lariviere,S.Morera
Key ref:
L.Larivière and S.Moréra (2004). Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase. J Biol Chem, 279, 34715-34720. PubMed id: 15178685 DOI: 10.1074/jbc.M404394200
Date:
31-Mar-04     Release date:   22-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04547  (GSTB_BPT4) -  DNA beta-glucosyltransferase
Seq:
Struc:
351 a.a.
351 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.27  - Dna beta-glucosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Transfers a beta-D-glucosyl residue from UDP-glucose to an hydroxymethylcytosine residue in DNA.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     viral reproduction   2 terms 
  Biochemical function     transferase activity     3 terms  

 

 
DOI no: 10.1074/jbc.M404394200 J Biol Chem 279:34715-34720 (2004)
PubMed id: 15178685  
 
 
Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase.
L.Larivière, S.Moréra.
 
  ABSTRACT  
 
Beta-glucosyltransferase (BGT) is a DNA-modifying enzyme and a glycosyltransferase. This inverting enzyme transfers glucose from UDP-glucose to the 5-hydroxymethyl cytosine bases of T4 phage DNA. From previous structural analyses we showed that Asp-100 and Asn-70 were, respectively, the catalytic base and the key residue for specific DNA recognition (Larivière, L., Gueguen-Chaignon, V., and Moréra, S. (2003) J. Mol. Biol. 330, 1077-1086). Here, we supply biochemical evidence supporting their essential roles in catalysis. We have also shown previously that BGT uses a base-flipping mechanism to access 5-hydroxymethyl cytosine (Larivière, L., and Moréra, S. (2002) J. Mol. Biol. 324, 483-490). Whether it is an active or a passive process remains unclear, as is the case for all DNA cleaving and modifying enzymes. Here, we report two crystal structures: (i) BGT in complex with a 13-mer DNA containing an A:G mismatch and (ii) BGT in a ternary complex with UDP and an oligonucleotide containing a single central G:C base pair. The binary structure reveals a specific complex with the flipped-out, mismatched adenine exposed to the active site. Unexpectedly, the other structure shows the non-productive binding of an intermediate flipped-out base. Our structural analysis provides clear evidence for a passive process.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. DNA contacts in the specific BGT-DNA structure. The DNA fragment interacts with three protein molecules. Two molecules (A and B) belong to the asymmetric unit, whereas the third is a crystal symmetric of molecule B. The N-terminal domain (residues 1 to 168 and the C-terminal helix) and the C-terminal domain (residues 169-337) are colored pink and slate, respectively. The DNA is shown in gold, with the flipped mismatched adenine in red. Molecule A is shown in ribbon representation, whereas Molecule B and its symmetric are shown in surface representation.
Figure 2.
FIG. 2. A, close-up view of the flipped-out mismatched adenine in a F[o] - F[c] omit map contoured at 2.5 . The opposite guanine (in atom colors) makes specific interactions with BGT, which are shown as broken lines. Residues and DNA are colored red and gold, respectively. B, identical view of the same region in the specific ternary complex with an abasic site at the target base in a F[o] - F[c] omit map contoured at 3 . C, similar view of the same region in the non-productive ternary complex. The terminal bases are both in extrahelical positions, and the flipped-out thymine is shown in a F[o] - F[c] omit map contoured at 2.5 . F71, Phe-71; F72, Phe-72; N70, Asn-70; R115, Arg-115.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 34715-34720) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21151123 C.X.Song, K.E.Szulwach, Y.Fu, Q.Dai, C.Yi, X.Li, Y.Li, C.H.Chen, W.Zhang, X.Jian, J.Wang, L.Zhang, T.J.Looney, B.Zhang, L.A.Godley, L.M.Hicks, B.T.Lahn, P.Jin, and C.He (2011).
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
  Nat Biotechnol, 29, 68-72.  
17284454 S.R.Bellamy, K.Krusong, and G.S.Baldwin (2007).
A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping.
  Nucleic Acids Res, 35, 1478-1487.  
15942026 T.J.Su, M.R.Tock, S.U.Egelhaaf, W.C.Poon, and D.T.Dryden (2005).
DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping.
  Nucleic Acids Res, 33, 3235-3244.  
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