6L0X

The First Tudor Domain of PHF20L1

Summary for 6L0X

• Entry DOI: 10.2210/pdb6l0x/pdb
• Descriptor: PHD finger protein 20-like protein 1, CITRIC ACID, GLYCEROL, ... (4 entities in total)
• Functional Keywords: phf20l1, tudor, apo, metal binding protein
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 18340.29

Authors

Lv, M.Q.,Gao, J. (deposition date: 2019-09-27, release date: 2020-09-23, Last modification date: 2023-11-22)

Primary citation

Lv, M.,Gao, J.,Li, M.,Ma, R.,Li, F.,Liu, Y.,Liu, M.,Zhang, J.,Yao, X.,Wu, J.,Shi, Y.,Tang, Y.,Pan, Y.,Zhang, Z.,Ruan, K.
Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1.
J Phys Chem Lett, 11:7932-7938, 2020

PubMed Abstract: The first Tudor domain (Tudor1) of PHF20L1 recognizes (non)histone methylation to play versatile roles. However, the underlying ligand-recognition mechanism remains unknown as a closed state revealed in the free-form structure. NMR relaxation dispersion and molecular dynamics simulations suggest a pre-existing low-population conformation with a remarkable rearrangement of aromatic cage residues of PHF20L1 Tudor1. Such an open-form conformation is utilized to recognize lysine 142 methylated DNMT1, a cosolvent, and an NMR fragment screening hit, as revealed by the complex crystal structures. Intriguingly, the ligand binding capacity was enhanced by mutation that tunes up the open-state population only. The recognition of DNMT1 by PHF20L1 was further validated in cancer cells. This conformational selection mechanism will enable the discovery of small molecule inhibitors against the seemingly "undruggable" PHF20L1 Tudor1.

PubMed: 32885980
DOI: 10.1021/acs.jpclett.0c02039

Experimental method

X-RAY DIFFRACTION (1.3 Å)