7CNR
Crystal structure of Thermococcus kodakaraensis aconitase X (apo-form)
Summary for 7CNR
| Entry DOI | 10.2210/pdb7cnr/pdb |
| Descriptor | DUF521 domain-containing protein, UPF0107 protein TK1248, FE3-S4 CLUSTER (3 entities in total) |
| Functional Keywords | mevalonate 5-phosphate dehydratase, lyase |
| Biological source | Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) More |
| Total number of polymer chains | 8 |
| Total formula weight | 226460.58 |
| Authors | Murase, Y.,Watanabe, Y.,Watanabe, S. (deposition date: 2020-08-03, release date: 2021-06-16, Last modification date: 2024-05-29) |
| Primary citation | Watanabe, S.,Murase, Y.,Watanabe, Y.,Sakurai, Y.,Tajima, K. Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily. Commun Biol, 4:687-687, 2021 Cited by PubMed Abstract: Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnX) and mevalonate 5-phosphate dehydratase (AcnX), respectively. We herein elucidated the crystal structures of AcnX from Agrobacterium tumefaciens (AtAcnX) and AcnX from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis. PubMed: 34099860DOI: 10.1038/s42003-021-02147-5 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.39 Å) |
Structure validation
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