Periplasmic dipeptide-binding protein: Difference between revisions

Pathogenic bacteria requirem several metal cofactors for enzymatic activity and, therein, performance of biochemical processes. As a result, these parasites have evolved mechanisms by which they can uptake essential nutrients from their host.  Though many of these ions are present in the cytosol of host cells or in the extracellular matrix of host tissue at various concentrations, thereby making sequestering these materials relatively simple, iron presents an interesting obstacle in terms of accessibility for bacteria in that it exists mainly in erythrocytes in the heme compound hemoglobin, though it also exists in storage compounds such as ferritin, lactoferrin, transferrin, and hemosiderin<ref>Ems, Thomas. “Biochemistry, Iron Absorption.” StatPearls [Internet]., U.S. National Library of  

Medicine, 21 Apr. 2019, www.ncbi.nlm.nih.gov/books/NBK448204/.</ref>. As a result, pathogens have evolved several means by which heme and hemoglobin can be uptaken by cells and degraded for abstraction of iron.

== M. Tuberculosis and Iron Uptake ==

M. Tuberculosis (Mtb) is a droplet-spread bacteria which causes tuberculosis. The bacterium lives and reproduces within the phagosomes of alveolar macrophages.  In 2018 alone, nearly 1.5 million people died from tuberculosis, making it among the top 10 diseases in terms of mortality<ref>“Tuberculosis (TB).” World Health Organization, World Health Organization,  

www.who.int/news-room/fact-sheets/detail/tuberculosis.</ref>.  Being that iron is relatively scarce within alveolar macrophage phagosomes, Mtb has evolved intricate means by which iron is uptaken.  The sheer number of genes dedicated to these processes is an indication of the complex evolution of this uptake.  For instance, M. tuberculosis have approximately 35 known genes alone associated only with the production of salicylate-derivative iron siderophores termed mycobactins<ref>DOI: 10.1086/518040</ref>.

== Heme Transport Into M. Tuberculosis ==

M. Tuberculosis has a two-membrane exterior, composed of a peptidoglycan exterior membrane and an interior cell membrane.  Heme transport into the periplasmic space has been understood for some time, relative to the recent developments pertaining to the DPP complex, in that several integral proteins used in the transport of heme from the extracellular matrix into the periplasmic space have been elucidated, specifically PPE36, PPE22, and PPE62<ref name=Alex>DOI: 10.1038/s41467-019-12109-5</ref>. The protein involved in the movement of heme through the periplasmic space, though, was unknown until September 2019, when the structure of DppA was elucidated.  DppA is a type of periplasmic binding protein specific to M. Tuberculosus.

Periplasmic binding proteins (PBPs) are non-enzymatic receptors that bacteria use to sense small molecules such as carbohydrates, amino acids, and ions, and transport them into the cytoplasm<ref name=ACS>DOI: 10.1021/cb900021q</ref>.  These sorts of proteins are ubiquitous in both gram-negative and gram-positive bacteria, appearing in gram-positive bacteria as membrane-anchored lipoproteins<ref name=ACS/>.  The glucose/galactose binding protein (<scene name='84/842887/Gbbp/4'>GBBP</scene>) of E. Coli is amongst the best studied of these proteins<ref>DOI: 10.1016/j.cbpa.2013.12.014</ref>.    These proteins typically exhibit a “Venus fly-trap” appearance, consisting of two globular domains connected by a small hinge region<ref name=ACS/>.  The hinge-like appearance is evident in GBBP.  These proteins often also work in conjunction with an ABC-binding cassette transporter which catalyzes the movement of the substance at hand across the cytoplasmic membrane.

Researchers have elucidated a few other heme binding PBPs which are functionally similar to DppA of Mtb. ShuT of S. dysenteriae and PhuT of P. aeruginosa were among the earliest of these proteins to be elucidated in 2007<ref name=Bob/>.  A general mechanism has been proposed for the activity of these proteins, but these proteins differ significantly structurally from DppA, so it is unlikely the specific mechanism of these proteins relates to DppA<ref name=Bob>DOI: 10.1074/jbc.M706761200</ref>.   

== DPP System in Mycobacterium Tuberculosis ==

Bacterial DppA proteins have signature Sec signal peptides specific to heme binding<ref name=Alex/>.  Research indicates the Sec signal peptide present on DppA of Mtb must be present for heme binding to occur<ref name=Alex/>.  DppA exhibits a much lower dissociation constant than other PBPs, around ~1.5 uM.  This is significantly less than functionally similar proteins such as Haemophilus influenzae’s HbpA or E. Coli’s DppA (HbpA = ~655 uM and DppA of E. Coli = ~10 uM)<ref name=Alex/>.

Crystal structure was obtained at 1.27Å resolution, with Rwork/free = 12.8/16.5%<ref name=Alex/>.  The structure shows a globular, heart-like appearance.  The tertiary structure is formed from two globular and mildly offset halves which are quite complementary.  The two halves fold onto each other, similar to two shells of a mollusk.

Other periplasmic binding proteins have been isolated and studied.  DppA shares no homology with HemT of S. marcescens<ref name=Alex/>.  The M. tuberculosis rv3666c-rv3663c operon, though, does encode four proteins that share ~25-45% sequence similarity with DPP dipeptide transporter of E. Coli, which similarly transports hemoglobin through the periplasmic space<ref name=Alex/>.

DppA is similar structurally to a few homologous proteins, especially to the S. typhimurium ortholog that superimposes the structure with an RMSD ~1.45Å<ref name=Alex/>.