PDBsum entry 3bmz

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Biosynthetic protein PDB id
Protein chains
185 a.a.
Waters ×680
PDB id:
Name: Biosynthetic protein
Title: Violacein biosynthetic enzyme vioe
Structure: Putative uncharacterized protein. Chain: a, b. Engineered: yes
Source: Chromobacterium violaceum. Organism_taxid: 243365. Strain: atcc 12472. Gene: vioe. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.21Å     R-factor:   0.169     R-free:   0.195
Authors: K.S.Ryan,C.L.Drennan
Key ref:
K.S.Ryan et al. (2008). The violacein biosynthetic enzyme VioE shares a fold with lipoprotein transporter proteins. J Biol Chem, 283, 6467-6475. PubMed id: 18171675 DOI: 10.1074/jbc.M708573200
13-Dec-07     Release date:   01-Jan-08    
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Protein chains
Pfam   ArchSchema ?
Q7NSZ5  (Q7NSZ5_CHRVO) -  Putative uncharacterized protein
191 a.a.
185 a.a.
Key:    PfamB domain  Secondary structure  CATH domain


DOI no: 10.1074/jbc.M708573200 J Biol Chem 283:6467-6475 (2008)
PubMed id: 18171675  
The violacein biosynthetic enzyme VioE shares a fold with lipoprotein transporter proteins.
K.S.Ryan, C.J.Balibar, K.E.Turo, C.T.Walsh, C.L.Drennan.
VioE, an unusual enzyme with no characterized homologues, plays a key role in the biosynthesis of violacein, a purple pigment with antibacterial and cytotoxic properties. Without bound cofactors or metals, VioE, from the bacterium Chromobacterium violaceum, mediates a 1,2 shift of an indole ring and oxidative chemistry to generate prodeoxyviolacein, a precursor to violacein. Our 1.21 A resolution structure of VioE shows that the enzyme shares a core fold previously described for lipoprotein transporter proteins LolA and LolB. For both LolB and VioE, a bound polyethylene glycol molecule suggests the location of the binding and/or active site of the protein. Mutations of residues near the bound polyethylene glycol molecule in VioE have identified the active site and five residues important for binding or catalysis. This structural and mutagenesis study suggests that VioE acts as a catalytic chaperone, using a fold previously associated with lipoprotein transporters to catalyze the production of its prodeoxyviolacein product.
  Selected figure(s)  
Figure 2.
FIGURE 2. Fold of VioE and structural comparisons. A, VioE crystallizes as a dimer, with the β-sheets positioned back-to-back. Chain A is shown in light blue, and chain B is shown in purple. A sigmaA-weighted 2F[o] - F[c] omit map that surrounds the PEG was generated by excluding PEG from the phase calculation, running 20 rounds of maximum likelihood refinement in Refmac and converting the structure factor file to a map file. Resulting density is shown in blue at 1.0 around the PEG modeled near each chain. β strands of chain B are numbered 1-11 based on their arrangement from the N to the C terminus of the protein; β3 is not visible from this view. B, one VioE monomer is shown, with β strands numbered 1-11 based on their arrangement from the N to the C terminus of the protein and with the C terminus labeled C-term. C, structurally aligned portions of VioE (purple), LolA (Protein Data Bank code 1UA8, green), and LolB (Protein Data Bank code 1IWM, blue) are shown, oriented identically to the VioE monomer shown in B. D-I, D and G show VioE (chain B), with arrows designating the loop region including amino acids 105-121 (in D) and the loop including amino acids 5-10 (in G), and with β strands numbered 1-11 based on their arrangement from the N to the C terminus of the protein and with the C terminus labeled C-term. E and H show LolA (Protein Data Bank code 1UA8), and F and I show LolB (Protein Data Bank code 1IWM). The models in D-F are identically positioned, and models in G-I are identically positioned. β-Strands are shown in blue, -helices and short 3[10] helices are shown in red, and loop regions are shown in green. The three -helices identified as forming a "lid" in LolA and LolB are labeled 1, 2, and 3. Figs. of protein models were prepared in PYMOL (, with secondary structure assignment carried out using DSSP (58).
Figure 3.
FIGURE 3. The putative lid and extended active site of VioE. A, the proposed closed lid region of LolA is shown (Protein Data Bank code 1UA8), with Arg^43 mediating a series of hydrogen-bonding interactions that close off the exposed side of the LolA structure. B, in VioE, the structurally superimposed residue to Arg^43 is Tyr^39, which is also positioned between β2 and β3 and also makes hydrogen bonding contacts to residues shown in blue. C, side chains within 6 Å of the PEG molecule of chain B are shown. Alternate conformations were refined for Ser^19, Met^160, and Ser^170. D, mutated residues are shown within the context of surrounding residues, each of which are within 12 Å from the bound PEG molecule. Residues that were not targeted for mutagenesis are shown in gray. Those in pink, when mutated, had no significant effect on the production of prodeoxyviolacein 3, whereas those in green, when mutated, had significantly reduced production of prodeoxyviolacein 3. In all panels, secondary structural elements are labeled in red.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 6467-6475) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21253897 M.Durán, A.Faljoni-Alario, and N.Durán (2010).
Chromobacterium violaceum and its important metabolites--review.
  Folia Microbiol (Praha), 55, 535-547.  
20490411 T.Mizuoka, K.Toume, M.Ishibashi, and T.Hoshino (2010).
Novel tryptophan metabolites, chromoazepinone A, B and C, produced by a blocked mutant of Chromobacterium violaceum, the biosynthetic implications and the biological activity of chromoazepinone A and B.
  Org Biomol Chem, 8, 3157-3163.  
19270402 H.Tokuda (2009).
Biogenesis of outer membranes in Gram-negative bacteria.
  Biosci Biotechnol Biochem, 73, 465-473.  
19389622 K.S.Ryan, and C.L.Drennan (2009).
Divergent pathways in the biosynthesis of bisindole natural products.
  Chem Biol, 16, 351-364.  
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.