6C2U | pdb_00006c2u

Solution structure of a phosphate-loop protein

• PDB DOI: https://doi.org/10.2210/pdb6C2U/pdb
• BMRB: 30394

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-09 Released: 2018-11-21 
• Deposition Author(s): Yang, F., Yang, W., Lin, Y.R., Romero Romero, M.L., Tawfik, D., Baker, D., Varani, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Simple yet functional phosphate-loop proteins.

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.

(2018) Proc Natl Acad Sci U S A 115: E11943-E11950

• PubMed: 30504143 
• DOI: https://doi.org/10.1073/pnas.1812400115
• Primary Citation Related Structures: 
  6C2U, 6C2V


• 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.

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Organizational Affiliation: 
• Department of Biomolecular Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel.
Department of Chemistry, University of Washington, Seattle, WA 98195-1700.
School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China.
Department of Biochemistry, University of Washington, Seattle, WA 98195-1700.
Department of Molecular Cell Biology and Genetics, Max Planck Institute, 01307 Dresden, Germany.
Bioinformatics Institute and Agency for Science, Technology and Research, 138671 Singapore.
Department of Biological Sciences, National University of Singapore, 117579 Singapore.
Computational Biology Unit and Department of Informatics, University of Bergen, N-5008 Bergen, Norway.
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894.
Department of Biomolecular Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 12.5 kDa 
• Atom Count: 877 
• Modeled Residue Count: 115 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphate-loop protein	A	115	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Yang, F., Yang, W., Lin, Y.R., Romero Romero, M.L., Tawfik, D., Baker, D., Varani, G.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2018-11-28
  Changes: Data collection, Database references
• Version 1.2: 2018-12-19
  Changes: Data collection, Database references
• Version 1.3: 2019-01-02
  Changes: Data collection, Database references
• Version 1.4: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.5: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.6: 2024-05-15
  Changes: Data collection, Database references