3AJE
Crystal structure of S. tokodaii Sua5 complexed with L-threonine and AMPPNP
Summary for 3AJE
| Entry DOI | 10.2210/pdb3aje/pdb |
| Related | 2EQA |
| Descriptor | Putative uncharacterized protein ST1526, THREONINE, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... (5 entities in total) |
| Functional Keywords | trna modification t6a, structural genomics, riken structural genomics/proteomics initiative, rsgi, rna binding protein |
| Biological source | Sulfolobus tokodaii |
| Cellular location | Cytoplasm (Potential): Q970S6 |
| Total number of polymer chains | 1 |
| Total formula weight | 39845.54 |
| Authors | Kuratani, M.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2010-06-01, release date: 2011-04-13, Last modification date: 2023-11-01) |
| Primary citation | Kuratani, M.,Kasai, T.,Akasaka, R.,Higashijima, K.,Terada, T.,Kigawa, T.,Shinkai, A.,Bessho, Y.,Yokoyama, S. Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP Proteins, 79:2065-2075, 2011 Cited by PubMed Abstract: The hypermodified nucleoside N(6)-threonylcarbamoyladenosine resides at position 37 of tRNA molecules bearing U at position 36 and maintains translational fidelity in the three kingdoms of life. The N(6)-threonylcarbamoyl moiety is composed of L-threonine and bicarbonate, and its synthesis was genetically shown to require YrdC/Sua5. YrdC/Sua5 binds to tRNA and ATP. In this study, we analyzed the L-threonine-binding mode of Sua5 from the archaeon Sulfolobus tokodaii. Isothermal titration calorimetry measurements revealed that S. tokodaii Sua5 binds L-threonine more strongly than L-serine and glycine. The Kd values of Sua5 for L-threonine and L-serine are 9.3 μM and 2.6 mM, respectively. We determined the crystal structure of S. tokodaii Sua5, complexed with AMPPNP and L-threonine, at 1.8 Å resolution. The L-threonine is bound next to AMPPNP in the same pocket of the N-terminal domain. Thr118 and two water molecules form hydrogen bonds with AMPPNP in a unique manner for adenine-specific recognition. The carboxyl group and the side-chain hydroxyl and methyl groups of L-threonine are buried deep in the pocket, whereas the amino group faces AMPPNP. The L-threonine is located in a suitable position to react together with ATP for the synthesis of N(6)-threonylcarbamoyladenosine. PubMed: 21538543DOI: 10.1002/prot.23026 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.8 Å) |
Structure validation
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