8T9Q

Crystal structure of fused YR, an asymmetric 4-OT trimer

Summary for 8T9Q

• Entry DOI: 10.2210/pdb8t9q/pdb
• Descriptor: Tautomerase (2 entities in total)
• Functional Keywords: isomerase, 4-ot, trimer, fused
• Biological source: Herbaspirillum; More
• Total number of polymer chains: 3
• Total formula weight: 46351.07

Authors

Moreno, R.Y.,Zhang, Y.J. (deposition date: 2023-06-24, release date: 2023-12-06)

Primary citation

Erwin, K.,Moreno, R.Y.,Baas, B.J.,Zhang, Y.J.,Whitman, C.P.
Introduction of Asymmetry in the Fused 4-Oxalocrotonate Tautomerases.
Biochemistry, 62:2461-2471, 2023

PubMed Abstract: Members of the 4-oxalocrotonate tautomerase (4-OT) subgroup in the tautomerase superfamily (TSF) are constructed from a single β-α-β unit and form homo- or heterohexamers, whereas those of the other four subgroups are composed of two consecutively joined β-α-β units and form trimers. A subset of sequences, double the length of the short 4-OTs, is found in the 4-OT subgroup. These "fused" 4-OTs form a separate subgroup that connects to the short 4-OTs in a sequence similarity network (SSN). The fused gene can be a template for the other four subgroups, resulting in the diversification of activity. Analysis of the SSN shows that multiple nodes in the fused 4-OTs connect to five linker nodes, which in turn connect to the short 4-OTs. Some fused 4-OTs are symmetric trimers and others are asymmetric trimers. The origin of this asymmetry was investigated by subjecting the sequences in three linker nodes and a closely associated fourth node to kinetic, mutagenic, and structural analyses. The results show that each sequence corresponds to the α- or β-subunit of a heterohexamer that functions as a 4-OT. Mutagenesis indicates that the key residues in both are αPro1 and βArg-11, like that of a typical 4-OT. Crystallographic analysis shows that both heterohexamers are asymmetric, where one heterodimer is flipped 180° relative to the other two heterodimers. The fusion of two subunits (α and β) of one asymmetric heterohexamer generates an asymmetric trimer with 4-OT activity. Hence, asymmetry can be introduced at the heterohexamer level and then retained in the fused trimers.

PubMed: 37490761
DOI: 10.1021/acs.biochem.3c00180

Experimental method

X-RAY DIFFRACTION (2.29 Å)