{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:10:45Z","timestamp":1785424245235,"version":"3.56.0"},"posted":{"date-parts":[[2026,5,20]]},"group-title":"Biochemistry","reference-count":33,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T00:00:00Z","timestamp":1779235200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["2515532"],"award-info":[{"award-number":["2515532"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"publisher"}]},{"award":["2515533"],"award-info":[{"award-number":["2515533"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"crossref","award":["T32GM136572"],"award-info":[{"award-number":["T32GM136572"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"award":["n\/a"],"award-info":[{"award-number":["n\/a"]}],"id":[{"id":"https:\/\/ror.org\/052csg198","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,5,20]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  <jats:italic>Caulobacter crescentus<\/jats:italic>\n                  is a gram-negative bacterium that produces the anionic sphingolipid ceramide diphosphoglycerate that can substitute for the lipopolysaccharide component of the outer membrane.\n                  <jats:italic>ccna_01210<\/jats:italic>\n                  is a gene in the operon for ceramide diphosphoglycerate synthesis and encodes for the enzyme, CpgD. CpgD is a magnesium-dependent CTP:phosphoglycerate cytidylyltransferase that catalyzes the synthesis of CDP-glycerate, and a pyrophosphate byproduct. CpgD displays substrate specificity for the nucleotide CTP and a preference for 2-phospho-D-glycerate over other phosphoglycerate enantiomers and isomers. Here, we present five high resolution structures for CpgD in various catalytic states that rationalize the specificity and preference of CpgD for its two substrates. This includes structures of apo CpgD, a CpgD-CTP-Mg\n                  <jats:sup>2+<\/jats:sup>\n                  ternary complex, and three CpgD-CDP-glycerate-pyrophosphate-Mg\n                  <jats:sup>2+<\/jats:sup>\n                  product bound complexes. The structures reveal CpgD nucleotide specificity is mediated by favorable hydrogen bonding interactions with the cytosine nucleobase of CTP, while the preference for 2-phospho-D-glycerate occurs due to favorable van der Waals interactions with the 2D enantiomer and unfavorable steric clashes with the 2L enantiomer. A catalytic mechanism involving a pentacoordinate transition state is proposed based on the observed stereochemical inversion of the \u03b1-phosphate in the substrate CTP in comparison to the \u03b1-phosphate of the product CDP-glycerate. Overall, this provides insights into the catalytic mechanism, nucleotide specificity, and enantiomeric substrate preference of the cytidylyltransferase CpgD that participates in a unique pathway of bacterial sphingolipid synthesis.\n                <\/jats:p>","DOI":"10.64898\/2026.05.18.725363","type":"posted-content","created":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T06:40:14Z","timestamp":1779345614000},"source":"Crossref","is-referenced-by-count":0,"title":["Van der Waals interactions mediate the enantiomeric substrate preference of the CTP:phosphoglycerate cytidylyltransferase CpgD"],"prefix":"10.64898","author":[{"given":"Rideeta","family":"Raquib","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook NY 11794, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanisha","family":"Dhakephalkar","sequence":"additional","affiliation":[{"name":"Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric A.","family":"Klein","sequence":"additional","affiliation":[{"name":"Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey, USA"},{"name":"Rutgers Center for Lipid Research, New Jersey Institute for Food Nutrition and Health, Rutgers University, New Brunswick, New Jersey, USA"},{"name":"Biology Department, Rutgers University-Camden, Camden, New Jersey, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4981-1253","authenticated-orcid":false,"given":"Michael V.","family":"Airola","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook NY 11794, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026052501450500000_2026.05.18.725363v1.1","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a000414"},{"key":"2026052501450500000_2026.05.18.725363v1.2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1611594113"},{"key":"2026052501450500000_2026.05.18.725363v1.3","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.73.11.7569-7577.2005"},{"key":"2026052501450500000_2026.05.18.725363v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/33046"},{"key":"2026052501450500000_2026.05.18.725363v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.110888"},{"key":"2026052501450500000_2026.05.18.725363v1.6","doi-asserted-by":"publisher","DOI":"10.1194\/jlr.R800012-JLR200"},{"key":"2026052501450500000_2026.05.18.725363v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-018-0055-5"},{"key":"2026052501450500000_2026.05.18.725363v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2019.04.002"},{"key":"2026052501450500000_2026.05.18.725363v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16274-w"},{"key":"2026052501450500000_2026.05.18.725363v1.10","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01919"},{"key":"2026052501450500000_2026.05.18.725363v1.11","doi-asserted-by":"crossref","unstructured":"Stankeviciute, G. , Guan, Z. , Goldfine, H. , and Klein, E. 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