7D2R

Crystal structure of Agrobacterium tumefaciens aconitase X mutant - S449C/C510V

Summary for 7D2R

• Entry DOI: 10.2210/pdb7d2r/pdb
• Descriptor: cis-3-hydroxy-L-proline dehydratase, FE2/S2 (INORGANIC) CLUSTER, GLYCEROL, ... (5 entities in total)
• Functional Keywords: cis-3-hydroxy-l-proline dehydratase, lyase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 1
• Total formula weight: 60938.99

Authors

Murase, Y.,Watanabe, Y.,Watanabe, S. (deposition date: 2020-09-17, 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

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: 34099860
DOI: 10.1038/s42003-021-02147-5

Experimental method

X-RAY DIFFRACTION (2.005 Å)