6C2V

Solution structure of a phosphate-loop protein

Summary for 6C2V

• Entry DOI: 10.2210/pdb6c2v/pdb
• Related: 6C2U
• NMR Information: BMRB: 30395
• Descriptor: phosphate-loop protein (1 entity in total)
• Functional Keywords: protein design, phosphate loop, ideal fold, grafting, de novo protein
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 12501.37

Authors

Yang, F.,Yang, W.,Lin, Y.R.,Romero Romero, M.L.,Tawfik, D.,Baker, D.,Varani, G. (deposition date: 2018-01-09, release date: 2018-11-21, Last modification date: 2024-05-15)

Primary citation

Romero Romero, M.L.,Yang, F.,Lin, Y.R.,Toth-Petroczy, A.,Berezovsky, I.N.,Goncearenco, A.,Yang, W.,Wellner, A.,Kumar-Deshmukh, F.,Sharon, M.,Baker, D.,Varani, G.,Tawfik, D.S.
Simple yet functional phosphate-loop proteins.
Proc. Natl. Acad. Sci. U.S.A., 115:E11943-E11950, 2018

PubMed Abstract: Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein's scaffold. Can motifs such as P-loops confer function in a simpler context? We applied a phylogenetic analysis that yielded a sequence logo of the putative ancestral Walker-A P-loop element: a β-strand connected to an α-helix via the P-loop. Computational design incorporated this element into de novo designed β-α repeat proteins with relatively few sequence modifications. We obtained soluble, stable proteins that unlike modern P-loop NTPases bound ATP in a magnesium-independent manner. Foremost, these simple P-loop proteins avidly bound polynucleotides, RNA, and single-strand DNA, and mutations in the P-loop's key residues abolished binding. Binding appears to be facilitated by the structural plasticity of these proteins, including quaternary structure polymorphism that promotes a combined action of multiple P-loops. Accordingly, oligomerization enabled a 55-aa protein carrying a single P-loop to confer avid polynucleotide binding. Overall, our results show that the P-loop Walker-A motif can be implemented in small and simple β-α repeat proteins, primarily as a polynucleotide binding motif.

PubMed: 30504143
DOI: 10.1073/pnas.1812400115

Experimental method

SOLUTION NMR