PDBsum entry 1q7e

Transferase

PDB id: 1q7e

Contents

Protein chain

410 a.a. *

Ligands

MET ×2

MPD ×7

Waters ×362

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of escherichia coli yfdw, A type III CoA transferase.

Authors

A.Gogos, J.Gorman, L.Shapiro.

Ref.

Acta Crystallogr D Biol Crystallogr, 2004, 60, 507-511. [DOI no: 10.1107/S0907444904000034]

PubMed id

14993676

Abstract

Crystal structures are reported for free and coenzyme A (CoA) bound forms of the YfdW protein from Escherichia coli, a representative type III CoA transferase. The structures reveal a two-domain protomer with interdomain connections forming a ring-like structure with a large central hole. Two protomers associate to form a highly intertwined dimer in which the hole of each ring is filled by the partner molecule. Each protomer binds a single CoA molecule and these CoA-binding sites are distant from one another in the dimer.

Figure 3.
Figure 3 Superposition of four YfdW structures: (i) apo form, shown in magenta, (ii) bound to CoA, shown in green, (iii) bound to acetyl-CoA (Gruez et al., 2003[Gruez, A., Roig-Zamboni, V., Valencia, C., Campanacci, V. & Cambillau, C. (2003). J. Biol. Chem. 278, 34582-34586.]), shown in cyan, and (iv) bound to acetyl-CoA and oxalate (Gruez et al., 2003[Gruez, A., Roig-Zamboni, V., Valencia, C., Campanacci, V. & Cambillau, C. (2003). J. Biol. Chem. 278, 34582-34586.]), shown in gray. CoA and acetyl-CoA are partly shown at the top of the picture, in blue and yellow, respectively. Oxalate is depicted in yellow at the bottom of the picture in an all-atom representation. Note the shift in conformation of the glycine-rich loop apparently induced by acetyl-CoA.

Figure 4.
Figure 4 Binding of CoA to the putative active site of YfdW. A CoA omit map contoured at 2 is shown in magenta. CoA is depicted in blue in an all-atom representation and the water molecules are shown as red spheres. All CoA interactions are within the large domain. The adenine moiety is positioned between the side chains of Arg38, Thr74, Phe97 and Met105. There are hydrogen-bonding interactions between adenine N6 and the carbonyl O atom of Leu72 and a water-mediated hydrogen bond between adenine N7 and the carbonyl O atom of Ile36. For the ribose moiety, O4' forms a hydrogen bond to Arg38 NH1 and O2' forms a water-mediated hydrogen bond to the carbonyl O atom of Ala101. The ribose phosphate moiety forms hydrogen bonds to His98 N 2 through O9 and O7 and to Lys75 N through O8. The binding of the CoA pantetheine chain is stabilized by van der Waals interactions with Met200 and several hydrogen-bonding interactions. AO1 of the pyrophosphate moiety hydrogen bonds to Arg38 N 2, AO4 to the hydroxyl of Tyr139 through two water molecules and AO5 to Lys137 N . The pantetheine hydroxyl group hydrogen bonds to the amide of His98 and the pantetheine amino PN4 interacts with the carbonyl O atom of Ala138 and PN8 with the carbonyl O atom of Asn96. The pantetheine carbonyl O atom PO5 interacts with Asn96 ND2, which is stabilized by a hydrogen bond to Ser18 OG. The pantetheine SH group PS1 hydrogen bonds to the amide of Asn17 and is also in close contact with Asp169 OD2. The SH group also appears to be stabilized by a helix dipole interaction with the N-terminus of -helix 1.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 507-511) copyright 2004.