Limits...
The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family.

Burman JD, Stevenson CE, Sawers RG, Lawson DM - BMC Struct. Biol. (2007)

Bottom Line: It has the trimeric quaternary structure and intersubunit cavities characteristic of this family of proteins.We show that TdcF is capable of binding several low molecular weight metabolites bearing a carboxylate group, although the interaction with 2-ketobutyrate appears to be the most well defined.These observations may be indicative of a role for TdcF in sensing this potentially toxic metabolite.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Chemistry, John Innes Centre, Norwich, UK. j.burman@bath.ac.uk <j.burman@bath.ac.uk>

ABSTRACT

Background: The YjgF/YER057c/UK114 family of proteins is widespread in nature, but has as yet no clearly defined biological role. Members of the family exist as homotrimers and are characterised by intersubunit clefts that are delineated by well-conserved residues; these sites are likely to be of functional significance, yet catalytic activity has never been detected for any member of this family. The gene encoding the TdcF protein of E. coli, a YjgF/YER057c/UK114 family member, resides in an operon that strongly suggests a role in the metabolism of 2-ketobutyrate for this protein.

Results: We have determined the crystal structure of E. coli TdcF by molecular replacement to a maximum resolution of 1.6 A. Structures are also presented of TdcF complexed with a variety of ligands.

Conclusion: The TdcF structure closely resembles those of all YjgF/YER057c/UK114 family members determined thus far. It has the trimeric quaternary structure and intersubunit cavities characteristic of this family of proteins. We show that TdcF is capable of binding several low molecular weight metabolites bearing a carboxylate group, although the interaction with 2-ketobutyrate appears to be the most well defined. These observations may be indicative of a role for TdcF in sensing this potentially toxic metabolite.

Show MeSH

Related in: MedlinePlus

Covalent modifications of TdcF. Stereoviews showing covalent modifications of TdcF. In both cases, 1.6 Å resolution 2mFobs - dFcalc electron density maps are shown contoured at approximately 1 sigma. (A) a fully oxidised cysteine (cysteine sulfonic acid) is observed at position 36 in each subunit of all structures; (B) a carboxylated lysine in two alternative conformations that is visible in only the A chain of the 2-ketobutyrate-bound structure. Figure generated using PyMOL [31].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1884159&req=5

Figure 6: Covalent modifications of TdcF. Stereoviews showing covalent modifications of TdcF. In both cases, 1.6 Å resolution 2mFobs - dFcalc electron density maps are shown contoured at approximately 1 sigma. (A) a fully oxidised cysteine (cysteine sulfonic acid) is observed at position 36 in each subunit of all structures; (B) a carboxylated lysine in two alternative conformations that is visible in only the A chain of the 2-ketobutyrate-bound structure. Figure generated using PyMOL [31].

Mentions: In the two structures determined at 1.6 Å resolution, inspection of the Fo-Fc electron density maps showed that, in all copies of Cys-36, the Sγ was surrounded by three peaks of positive density, that were too close to the atom to represent water molecules. This was modelled as a fully oxidised cysteine ie. cysteine sulfonic acid (Cys-SO3H), which gave a good fit to the electron density after refinement (Figure 6A). It was subsequently shown that cysteine sulfonic acid refined well at these positions in the two lower resolution structures as well. This modification is currently present in some 38 entries in the Protein Data Bank but is likely to be present, though undetected, in other structures determined at medium to low resolution. The fact that the residue is fully oxidised suggests that it is unusually reactive, but since this modification is generally irreversible, it is most likely of no biological significance. Furthermore, this residue is highly variable in the YjgF/YER057c/UK114 family, and it occurs in a surface loop of the protein, the Sγ being approximately 15 Å away from the nearest 2-ketobutyrate.


The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family.

Burman JD, Stevenson CE, Sawers RG, Lawson DM - BMC Struct. Biol. (2007)

Covalent modifications of TdcF. Stereoviews showing covalent modifications of TdcF. In both cases, 1.6 Å resolution 2mFobs - dFcalc electron density maps are shown contoured at approximately 1 sigma. (A) a fully oxidised cysteine (cysteine sulfonic acid) is observed at position 36 in each subunit of all structures; (B) a carboxylated lysine in two alternative conformations that is visible in only the A chain of the 2-ketobutyrate-bound structure. Figure generated using PyMOL [31].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1884159&req=5

Figure 6: Covalent modifications of TdcF. Stereoviews showing covalent modifications of TdcF. In both cases, 1.6 Å resolution 2mFobs - dFcalc electron density maps are shown contoured at approximately 1 sigma. (A) a fully oxidised cysteine (cysteine sulfonic acid) is observed at position 36 in each subunit of all structures; (B) a carboxylated lysine in two alternative conformations that is visible in only the A chain of the 2-ketobutyrate-bound structure. Figure generated using PyMOL [31].
Mentions: In the two structures determined at 1.6 Å resolution, inspection of the Fo-Fc electron density maps showed that, in all copies of Cys-36, the Sγ was surrounded by three peaks of positive density, that were too close to the atom to represent water molecules. This was modelled as a fully oxidised cysteine ie. cysteine sulfonic acid (Cys-SO3H), which gave a good fit to the electron density after refinement (Figure 6A). It was subsequently shown that cysteine sulfonic acid refined well at these positions in the two lower resolution structures as well. This modification is currently present in some 38 entries in the Protein Data Bank but is likely to be present, though undetected, in other structures determined at medium to low resolution. The fact that the residue is fully oxidised suggests that it is unusually reactive, but since this modification is generally irreversible, it is most likely of no biological significance. Furthermore, this residue is highly variable in the YjgF/YER057c/UK114 family, and it occurs in a surface loop of the protein, the Sγ being approximately 15 Å away from the nearest 2-ketobutyrate.

Bottom Line: It has the trimeric quaternary structure and intersubunit cavities characteristic of this family of proteins.We show that TdcF is capable of binding several low molecular weight metabolites bearing a carboxylate group, although the interaction with 2-ketobutyrate appears to be the most well defined.These observations may be indicative of a role for TdcF in sensing this potentially toxic metabolite.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Chemistry, John Innes Centre, Norwich, UK. j.burman@bath.ac.uk <j.burman@bath.ac.uk>

ABSTRACT

Background: The YjgF/YER057c/UK114 family of proteins is widespread in nature, but has as yet no clearly defined biological role. Members of the family exist as homotrimers and are characterised by intersubunit clefts that are delineated by well-conserved residues; these sites are likely to be of functional significance, yet catalytic activity has never been detected for any member of this family. The gene encoding the TdcF protein of E. coli, a YjgF/YER057c/UK114 family member, resides in an operon that strongly suggests a role in the metabolism of 2-ketobutyrate for this protein.

Results: We have determined the crystal structure of E. coli TdcF by molecular replacement to a maximum resolution of 1.6 A. Structures are also presented of TdcF complexed with a variety of ligands.

Conclusion: The TdcF structure closely resembles those of all YjgF/YER057c/UK114 family members determined thus far. It has the trimeric quaternary structure and intersubunit cavities characteristic of this family of proteins. We show that TdcF is capable of binding several low molecular weight metabolites bearing a carboxylate group, although the interaction with 2-ketobutyrate appears to be the most well defined. These observations may be indicative of a role for TdcF in sensing this potentially toxic metabolite.

Show MeSH
Related in: MedlinePlus