5C3R

Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG and 5-hydroxymethyluracil (5hmU)

Summary for 5C3R

• Entry DOI: 10.2210/pdb5c3r/pdb
• Related: 5C3O 5C3P 5C3Q 5C3S
• Descriptor: Thymine dioxygenase, NICKEL (II) ION, 2-OXOGLUTARIC ACID, ... (6 entities in total)
• Functional Keywords: dioxygenase, substrate b, dsbh fold, oxidoreductase
• Biological source: Neurospora crassa
• Total number of polymer chains: 4
• Total formula weight: 156347.47

Authors

Li, W.,Zhang, T.,Ding, J. (deposition date: 2015-06-17, release date: 2015-10-21, Last modification date: 2023-11-08)

Primary citation

Li, W.,Zhang, T.,Ding, J.
Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi
Nucleic Acids Res., 43:10026-10038, 2015

PubMed Abstract: TET proteins play a vital role in active DNA demethylation in mammals and thus have important functions in many essential cellular processes. The chemistry for the conversion of 5mC to 5hmC, 5fC and 5caC catalysed by TET proteins is similar to that of T to 5hmU, 5fU and 5caU catalysed by thymine-7-hydroxylase (T7H) in the nucleotide anabolism in fungi. Here, we report the crystal structures and biochemical properties of Neurospora crassa T7H. T7H can bind the substrates only in the presence of cosubstrate, and binding of different substrates does not induce notable conformational changes. T7H exhibits comparable binding affinity for T and 5hmU, but 3-fold lower affinity for 5fU. Residues Phe292, Tyr217 and Arg190 play critical roles in substrate binding and catalysis, and the interactions of the C5 modification group of substrates with the cosubstrate and enzyme contribute to the slightly varied binding affinity and activity towards different substrates. After the catalysis, the products are released and new cosubstrate and substrate are reloaded to conduct the next oxidation reaction. Our data reveal the molecular basis for substrate specificity and catalytic mechanism of T7H and provide new insights into the molecular mechanism of substrate recognition and catalysis of TET proteins.

PubMed: 26429971
DOI: 10.1093/nar/gkv979

Experimental method

X-RAY DIFFRACTION (2.35 Å)