8T8K

Structure of Domain of Unknown Function 507 (DUF507) in Space Group C222(1)

Summary for 8T8K

• Entry DOI: 10.2210/pdb8t8k/pdb
• Descriptor: DUF507 family protein, HEXANE-1,6-DIOL (3 entities in total)
• Functional Keywords: duf507, 4-helix bundle, unknown function
• Biological source: Aquifex aeolicus
• Total number of polymer chains: 1
• Total formula weight: 22057.73

Authors

Tanner, J.J.,McKay, C.E. (deposition date: 2023-06-22, release date: 2023-08-30)

Primary citation

McKay, C.E.,Cheng, J.,Tanner, J.J.
Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold.
Sci Rep, 13:13496-13496, 2023

PubMed Abstract: The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus is reported (AaDUF507, UniProt O67633, 183 residues). The structure was determined in two space groups (C222 and P321) at 1.9 Å resolution. The phase problem was solved by molecular replacement using an AlphaFold model as the search model. AaDUF507 is a Y-shaped α-helical protein consisting of an anti-parallel 4-helix bundle base and two helical arms that extend 30-Å from the base. The two crystal structures differ by a 25° rigid body rotation of the C-terminal arm. The tertiary structure exhibits pseudo-twofold symmetry. The structural symmetry mirrors internal sequence similarity: residues 11-57 and 102-148 are 30% identical and 53% similar with an E-value of 0.002. In one of the structures, electron density for an unknown ligand, consistent with nicotinamide or similar molecule, may indicate a functional site. Docking calculations suggest potential ligand binding hot spots in the region between the helical arms. Structure-based query of the Protein Data Bank revealed no other protein with a similar tertiary structure, leading us to propose that AaDUF507 represents a new protein fold.

PubMed: 37596303
DOI: 10.1038/s41598-023-40558-y

Experimental method

X-RAY DIFFRACTION (1.88 Å)