{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T12:24:04Z","timestamp":1785414244953,"version":"3.56.0"},"posted":{"date-parts":[[2026,1,31]]},"group-title":"Biochemistry","reference-count":37,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T00:00:00Z","timestamp":1769817600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"id":[{"id":"https:\/\/ror.org\/006w34k90","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,1,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  BmpA is a putative substrate-binding protein from\n                  <jats:italic>Borrelia burgdorferi<\/jats:italic>\n                  , the causative agent of Lyme disease, an organism with limited metabolic capacity that relies on salvage pathways rather than\n                  <jats:italic>de novo<\/jats:italic>\n                  nucleotide biosynthesis. Here, we determine the crystal structure of BmpA to a resolution of 2.6 \u00c5, revealing a conserved substrate-binding protein fold with a deeply buried nucleoside-binding pocket. Using microscale thermophoresis, we show that BmpA binds thymidine with high affinity followed by cytidine and adenosine, whereas binding to ribose, guanosine, inosine, and uridine was not detected. Structure-guided mutagenesis further demonstrates that two conserved aromatic residues (Phe27 and Phe176) are essential for thymidine recognition, as alanine substitution at either position abolishes detectable binding. Additionally, a Foldseek-based structural homology search identified related proteins across diverse bacterial and archaeal species that share a conserved overall fold and binding-site architecture despite low sequence similarity, consistent with an evolutionarily conserved scaffold that can accommodate distinct nucleoside ligands. Together, our work illustrates how conserved binding protein architectures enable selective nucleoside acquisition and provides a foundation for understanding nutrient uptake strategies in organisms with reduced genomes.\n                <\/jats:p>","DOI":"10.64898\/2026.01.30.702971","type":"posted-content","created":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T04:20:12Z","timestamp":1769919612000},"source":"Crossref","is-referenced-by-count":0,"title":["Structure and ligand specificity of\n                  <i>Borrelia burgdorferi<\/i>\n                  BmpA"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-5604-8352","authenticated-orcid":false,"given":"Qianqiao","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Biology, Stanford University, Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor A.","family":"Nu\u00f1ez","sequence":"additional","affiliation":[{"name":"Department of Structural Biology, Stanford University, Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Fernandez","sequence":"additional","affiliation":[{"name":"Macromolecular Structure Group, Nucleus at Sarafan ChEM-H, Stanford University, Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naima G.","family":"Sharaf","sequence":"additional","affiliation":[{"name":"Department of Biology, Stanford University, Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026020510570038000_2026.01.30.702971v1.1","doi-asserted-by":"crossref","first-page":"3467","DOI":"10.1128\/iai.63.9.3467-3472.1995","article-title":"Adherence of Borrelia burgdorferi to the proteoglycan decorin","volume":"63","year":"1995","journal-title":"Infection and Immunity"},{"key":"2026020510570038000_2026.01.30.702971v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-020-0400-5"},{"key":"2026020510570038000_2026.01.30.702971v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2016.65"},{"key":"2026020510570038000_2026.01.30.702971v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/37551"},{"key":"2026020510570038000_2026.01.30.702971v1.5","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1128\/CDLI.12.8.935-940.2005","article-title":"Borrelia burgdorferi BmpA, BmpB, and BmpD proteins are expressed in human infection and contribute to P39 immunoblot reactivity in patients with Lyme disease","volume":"12","year":"2005","journal-title":"Clinical and Vaccine Immunology"},{"key":"2026020510570038000_2026.01.30.702971v1.6","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1128\/jcm.29.2.236-243.1991","article-title":"Antibody to a 39-kilodalton Borrelia burgdorferi antigen (P39) as a marker for infection in experimentally and naturally inoculated animals","volume":"29","year":"1991","journal-title":"Journal of Clinical Microbiology"},{"key":"2026020510570038000_2026.01.30.702971v1.7","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.33.2.419-427.1995"},{"key":"2026020510570038000_2026.01.30.702971v1.8","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/167.2.392"},{"key":"2026020510570038000_2026.01.30.702971v1.9","unstructured":"Centers for Disease Control and Prevention Standard Two-Tier Lyme Disease Testing Suggested Result Reporting Interpretation. 2024; 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others Deciphering cellodextrin and glucose uptake in Clostridium thermocellum","volume":"13","year":"2022","journal-title":"MBio"},{"key":"2026020510570038000_2026.01.30.702971v1.21","doi-asserted-by":"crossref","unstructured":"Abdullah, M. 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Pathogens 2020, 9, 678.","DOI":"10.3390\/pathogens9090678"},{"key":"2026020510570038000_2026.01.30.702971v1.28","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.69742"},{"key":"2026020510570038000_2026.01.30.702971v1.29","doi-asserted-by":"crossref","first-page":"110493","DOI":"10.1016\/j.jbc.2025.110493","article-title":"Two stages of substrate discrimination dictate selectivity in theE. coliMetNI-Q ABC transporter system","volume":"301","year":"2025","journal-title":"Journal of Biological Chemistry"},{"key":"2026020510570038000_2026.01.30.702971v1.30","doi-asserted-by":"crossref","unstructured":"Kabsch, W. XDS . 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