1. Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain
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Lukasz Jaroszewski, Dustin C. Ernst, Keith O. Hodgson, Lian Duan, Tamara Astakhova, Abhinav Kumar, Tiffany Wooten, Michelle Chiu, Julie Feuerhelm, Edward Nigoghossian, Daniel McMullan, Gye Won Han, Qingping Xu, Christine B Trame, Linda Okach, Debanu Das, Herbert L. Axelrod, Polat Abdubek, Heath E. Klock, Carol L. Farr, Mitchell D. Miller, Sanjay Krishna, Alex Bateman, Henry van den Bedem, Anna Grzechnik, David Marciano, Thomas Clayton, Marc C. Deller, Connie Chen, Christopher L. Rife, Natasha Sefcovic, John Wooley, Constantina Bakolitsa, Kevin K. Jin, Hsiu-Ju Chiu, Amanda Nopakun, Marc André Elsliger, Andrew T. Morse, Dennis Carlton, Ian A. Wilson, Christina Puckett, Adam Godzik, Ashley M. Deacon, Kyle Ellrott, Joanna C Grant, Robert D. Finn, Dana Weekes, Piotr Kozbial, Henry J Tien, Mark W. Knuth, Ron Reyes, and Scott A. Lesley
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Models, Molecular ,asu, asymmetric unit ,Protein Data Bank (RCSB PDB) ,SSRL, Stanford Synchrotron Radiation Lightsource ,Crystallography, X-Ray ,Protein Structure, Secondary ,chemistry.chemical_compound ,PH, Pleckstrin homology ,Structural Biology ,Pleckstrin homology (PH) domain ,Conserved Sequence ,0303 health sciences ,030302 biochemistry & molecular biology ,bacterial PH domain (PHb) ,Pleckstrin homology domain ,Eukaryotic Cells ,Biochemistry ,Domain (ring theory) ,TCEP ,higher-order symmetry ,DUF1696, domain of unknown function family 1696 ,lipids (amino acids, peptides, and proteins) ,VPS36, vacuolar protein sorting protein 36 ,Protein Binding ,Protein family ,Surface Properties ,Stereochemistry ,Molecular Sequence Data ,PTB, phosphotyrosine binding ,protein assembly ,Biology ,Ring (chemistry) ,Article ,TEV, tobacco etch virus ,Structural genomics ,Evolution, Molecular ,03 medical and health sciences ,TCEP, tris(2-carboxyethyl)phosphine–HCl ,Bacterial Proteins ,PDB, Protein Data Bank ,MAD, multiwavelength anomalous diffraction ,ALS, Advanced Light Source ,Amino Acid Sequence ,Protein Structure, Quaternary ,PIPE, Polymerase Incomplete Primer Extension ,protein evolution ,Molecular Biology ,PEG, polyethylene glycol ,030304 developmental biology ,Binding Sites ,Bacteria ,Sequence Homology, Amino Acid ,biology.organism_classification ,Protein Structure, Tertiary ,JCSG, Joint Center for Structural Genomics ,Prokaryotic Cells ,chemistry ,PHb, bacterial PH domain ,Sequence Alignment - Abstract
Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C5 symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C12 symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the β-strands of adjacent protomers that likely mediates protein–protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged.
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