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<table width="95%" border="0"><tr><td>
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==Cryo-EM structure of human SLC22A6 (OAT1) in the apo-state==
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{| align="left"
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<StructureSection load='9kkk' size='340' side='right'caption='[[9kkk]], [[Resolution|resolution]] 3.85&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[9kkk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9KKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9KKK FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.85&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9kkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9kkk OCA], [https://pdbe.org/9kkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9kkk RCSB], [https://www.ebi.ac.uk/pdbsum/9kkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9kkk ProSAT]</span></td></tr>
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</table>
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<span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR </b></span>
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== Function ==
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[https://www.uniprot.org/uniprot/S22A6_HUMAN S22A6_HUMAN] Secondary active transporter that functions as a Na(+)-independent organic anion (OA)/dicarboxylate antiporter where the uptake of one molecule of OA into the cell is coupled with an efflux of one molecule of intracellular dicarboxylate such as 2-oxoglutarate or glutarate (PubMed:11669456, PubMed:11907186, PubMed:14675047, PubMed:22108572, PubMed:23832370, PubMed:28534121, PubMed:9950961). Mediates the uptake of OA across the basolateral side of proximal tubule epithelial cells, thereby contributing to the renal elimination of endogenous OA from the systemic circulation into the urine (PubMed:9887087). Functions as a biopterin transporters involved in the uptake and the secretion of coenzymes tetrahydrobiopterin (BH4), dihydrobiopterin (BH2) and sepiapterin to urine, thereby determining baseline levels of blood biopterins (PubMed:28534121). Transports prostaglandin E2 (PGE2) and prostaglandin F2-alpha (PGF2-alpha) and may contribute to their renal excretion (PubMed:11907186). Also mediates the uptake of cyclic nucleotides such as cAMP and cGMP (PubMed:26377792). Involved in the transport of neuroactive tryptophan metabolites kynurenate (KYNA) and xanthurenate (XA) and may contribute to their secretion from the brain (PubMed:22108572, PubMed:23832370). May transport glutamate (PubMed:26377792). Also involved in the disposition of uremic toxins and potentially toxic xenobiotics by the renal organic anion secretory pathway, helping reduce their undesired toxicological effects on the body (PubMed:11669456, PubMed:14675047). Uremic toxins include the indoxyl sulfate (IS), hippurate/N-benzoylglycine (HA), indole acetate (IA), 3-carboxy-4- methyl-5-propyl-2-furanpropionate (CMPF) and urate (PubMed:14675047, PubMed:26377792). Xenobiotics include the mycotoxin ochratoxin (OTA) (PubMed:11669456). May also contribute to the transport of organic compounds in testes across the blood-testis-barrier (PubMed:35307651).<ref>PMID:11669456</ref> <ref>PMID:11907186</ref> <ref>PMID:14675047</ref> <ref>PMID:22108572</ref> <ref>PMID:23832370</ref> <ref>PMID:26377792</ref> <ref>PMID:28534121</ref> <ref>PMID:35307651</ref> <ref>PMID:9887087</ref> <ref>PMID:9950961</ref>
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<div style="background-color:#fffaf0;">
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<span style="font-size:120%">
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== Publication Abstract from PubMed ==
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Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen
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The organic anion transporter 1 (OAT1) plays a key role in excreting waste from organic drug metabolism and contributes significantly to drug-drug interactions and drug disposition. However, the structural basis of specific substrate and inhibitor transport by human OAT1 (hOAT1) has remained elusive. We determined four cryogenic electron microscopy (cryo-EM) structures of hOAT1 in its inward-facing conformation: the apo form, the substrate (olmesartan)-bound form with different anions, and the inhibitor (probenecid)-bound form. Structural and functional analyses revealed that Ser203 has an auxiliary role in chloride coordination, and it is a critical residue modulating olmesartan transport via chloride ion interactions. Structural comparisons indicate that inhibitors not only compete with substrates, but also obstruct substrate exit and entry from the cytoplasmic side, thereby increasing inhibitor retention. The findings can support drug development by providing insights into substrate recognition and the mechanism by which inhibitors arrest the OAT1 transport cycle.
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PNAS,  March 6, 2025, Vol. 122  No. 10 e2426324122, [https://doi.org/10.1073/pnas.2426324122] 
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</span>
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</td></tr></table>
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==Structure Tour==
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<StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''>
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===Abstract===
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The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.
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===Overall Structure of NolR===
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NolR is a member of the '''ArsR/SmtB family''' of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.
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Click on "<scene name='85/857155/Chain_a/2'>Chain A</scene>" of "NolR".
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Click on "<scene name='85/857155/Chain_b/2'>Chain B</scene>" of "NolR".
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* '''Dimerization:''' Two alpha-helices (<scene name='85/857155/Alpha_1_and_alpha_5/1'>alpha-1 and alpha-5)</scene> from each monomer form a coiled-coil dimerization interface.
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* '''DNA Binding Domain:''' A triangular set of helices (<scene name='85/857155/Alpha_2_and_alpha_4/1'>alpha-2 and alpha-4</scene>) positions the recognition helix (<scene name='85/857155/Alpha3_alpha4/1'>alpha-3 and alpha-4</scene>) for interaction with the DNA major groove.
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* '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.
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===DNA Binding and Recognition===
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The co-crystal structure of NolR with a 22-base pair operator sequence (<scene name='85/857155/Dna/1'>Oligo AT</scene>) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.
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Select <scene name='85/857155/Dna_binding/1'>DNA binding</scene> to visualize the binding of NolR on oligo AT rich DNA.
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* '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.
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* '''Minor Groove:''' The beta-wing residues contact the minor groove.
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* '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.
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* '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.
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===The Gln56 Conformational Switch===
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A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).
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Click <scene name='85/857155/Gln56_switch/1'>Gln56 switch</scene> to visualize the Gln56 residues that are essential for the variable binding of NolR.
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* '''Consensus Binding (Oligo AT):''' In the first half-site, '''Gln56''' hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.
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* '''Variable Binding (Oligo AA):''' When bound to the Oligo AA sequence (where T7' is replaced by A7'), '''Gln56''' undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.
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===References===
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* Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.
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===About this Page===
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<!-- This section ensures you get credit -->
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This page was created by '''[[User:Your_Username|Balagopal Nithin]]'''.<br>
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University/Institution Name (Indian Institute of Science Education and Research,Pune)
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Cryo-EM structures of human OAT1 reveal drug binding and inhibition mechanisms.,Jeon HM, Eun J, Kim KH, Kim Y Structure. 2025 Aug 14:S0969-2126(25)00267-9. doi: 10.1016/j.str.2025.07.019. PMID:40845848<ref>PMID:40845848</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 9kkk" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
</StructureSection>
</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Eun J]]
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[[Category: Jeon HM]]
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[[Category: Kim Y]]

Revision as of 17:49, 29 November 2025

Cryo-EM structure of human SLC22A6 (OAT1) in the apo-state

PDB ID 9kkk

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