Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Substrate specificity and transport mechanism of the chloroplast dicarboxylate transporters DiT1 and DiT2.
Journal, issue, pages	Plant Cell, Year 2026
Publish date	Feb 23, 2026
Authors	Zhao Yang / Xue Zhang / Jingtao Zheng / Shunhao Zhou / Ming-Ju Amy Lyu / Miaolian Ma / Xin-Guang Zhu / Fang Yu / Peng Zhang /
PubMed Abstract	Dicarboxylate transporters (DiTs) mediate the exchange of dicarboxylates across the chloroplast inner membrane, playing critical roles in C/N coupling, photorespiration, chloroplast redox ...Dicarboxylate transporters (DiTs) mediate the exchange of dicarboxylates across the chloroplast inner membrane, playing critical roles in C/N coupling, photorespiration, chloroplast redox homeostasis, and C4 photosynthesis. DiT1 and DiT2 are Na⁺-independent exchangers of the solute carrier 13 (SLC13) family, and exhibit overlapping yet distinct substrate specificities: DiT1 transports 2-oxoglutarate, malate, and oxaloacetate, while DiT2 additionally transports glutamate and aspartate. However, the structural determinants of their substrate specificity and transport mechanism remain unclear. Here we determined cryo-electron microscopy structures of Arabidopsis thaliana DiT1 and DiT2.1 bound to diverse substrates in dual conformational states. Structural analyses revealed that AtDiT1 possesses a singular dicarboxylate-binding site that is electrostatically incompatible with amino acid substrates, whereas AtDiT2.1 has two distinct sites to accommodate C4- and C5-dicarboxylates, thus allowing amino acids to bind without electrostatic repulsion. Phylogenetic analysis identified an A226S substitution in the substrate-binding site of DiT1, emerging during evolution in the charophyte ancestor of land plants. This substitution enhances oxaloacetate binding affinity in DiT1, which may have improved adaptation to terrestrial environments. Additionally, two conserved positively charged residues in DiTs functionally mimic Na⁺ used by SLC13 co-transporters, thereby enabling a Na⁺-independent elevator-type transport mechanism. These findings provide critical structural and mechanistic insights into the functional divergence of plant DiTs.
External links	Plant Cell / PubMed:41731698
Methods	EM (single particle)
Resolution	2.41 - 2.94 Å
Structure data	63803 9mcr EMDB-63803, PDB-9mcr: Plant chloroplast dicarboxylate transporter AtDiT1 Method: EM (single particle) / Resolution: 2.41 Å 63804 9mcs EMDB-63804, PDB-9mcs: Plant chloroplast dicarboxylate transporter AtDiT1 bound with OAA Method: EM (single particle) / Resolution: 2.51 Å 63805 9mct EMDB-63805, PDB-9mct: Plant chloroplast dicarboxylate transporter AtDiT1 bound with 2-OG Method: EM (single particle) / Resolution: 2.94 Å 63806 9mcu EMDB-63806, PDB-9mcu: Plant chloroplast dicarboxylate transporter AtDiT2.1 Method: EM (single particle) / Resolution: 2.69 Å 63807 9mcv EMDB-63807, PDB-9mcv: Plant chloroplast dicarboxylate transporter AtDiT2.1 bound with malate Method: EM (single particle) / Resolution: 2.72 Å 63808 9u32 EMDB-63808, PDB-9u32: Plant chloroplast dicarboxylate transporter AtDiT2.1 bound with Glu Method: EM (single particle) / Resolution: 2.51 Å
Chemicals	ChemComp-OAA: OXALOACETATE ION ChemComp-HOH: WATER ChemComp-AKG: 2-OXOGLUTARIC ACID ChemComp-Y01: CHOLESTEROL HEMISUCCINATE ChemComp-LMR: (2S)-2-hydroxybutanedioic acid ChemComp-GLU: GLUTAMIC ACID
Source	arabidopsis thaliana (thale cress)
Keywords	TRANSPORT PROTEIN / chloroplast / dicarboxylate transporters / C/N coupling / C4 photosynthesis