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Mol. Cells 2009; 27(1): 99-103

Published online January 31, 2009

https://doi.org/10.1007/s10059-009-0010-6

© The Korean Society for Molecular and Cellular Biology

Crystal Structures of Substrate and Inhibitor Complexes of Ribose 5-Phosphate Isomerase A from Vibrio vulnificus YJ016

Tae Gyun Kim, Taek Hun Kwon, Kyoungin Min, Mi-Sook Dong, Young In Park and Changill Ban

Received: October 21, 2008; Accepted: October 28, 2008

Abstract

Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. We have determined the crystal structures of the open form RpiA from Vibrio vulnificus YJ106 (VvRpiA) in complex with the R5P and the closed form with arabinose-5-phosphate (A5P) in parallel with the apo VvRpiA at 2.0 ? resolution. VvRpiA is highly similar to Escherichia coli RpiA, and the VvRpiA-R5P complex strongly resembles the E. coli RpiA-A5P complex. Interestingly, unlike the E. coli RpiA-A5P complex, the position of A5P in the VvRpiA-A5P complex reveals a different position than the R5P binding mode. VvRpiA-A5P has a sugar ring inside the binding pocket and a phosphate group outside the binding pocket: By contrast, the sugar ring of A5P interacts with the Asp4, Lys7, Ser30, Asp118, and Lys121 residues; the phosphate group of A5P interacts with two water molecules, W51 and W82.

Keywords Arabinose-5-phosphate, crystal structure, E. coli RpiA, Ribose-5-phosphate isomerase A (RpiA), Vibrio vulnificus YJ016.

Article

Research Article

Mol. Cells 2009; 27(1): 99-103

Published online January 31, 2009 https://doi.org/10.1007/s10059-009-0010-6

Copyright © The Korean Society for Molecular and Cellular Biology.

Crystal Structures of Substrate and Inhibitor Complexes of Ribose 5-Phosphate Isomerase A from Vibrio vulnificus YJ016

Tae Gyun Kim, Taek Hun Kwon, Kyoungin Min, Mi-Sook Dong, Young In Park and Changill Ban

Received: October 21, 2008; Accepted: October 28, 2008

Abstract

Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. We have determined the crystal structures of the open form RpiA from Vibrio vulnificus YJ106 (VvRpiA) in complex with the R5P and the closed form with arabinose-5-phosphate (A5P) in parallel with the apo VvRpiA at 2.0 ? resolution. VvRpiA is highly similar to Escherichia coli RpiA, and the VvRpiA-R5P complex strongly resembles the E. coli RpiA-A5P complex. Interestingly, unlike the E. coli RpiA-A5P complex, the position of A5P in the VvRpiA-A5P complex reveals a different position than the R5P binding mode. VvRpiA-A5P has a sugar ring inside the binding pocket and a phosphate group outside the binding pocket: By contrast, the sugar ring of A5P interacts with the Asp4, Lys7, Ser30, Asp118, and Lys121 residues; the phosphate group of A5P interacts with two water molecules, W51 and W82.

Keywords: Arabinose-5-phosphate, crystal structure, E. coli RpiA, Ribose-5-phosphate isomerase A (RpiA), Vibrio vulnificus YJ016.

Mol. Cells
Jul 31, 2022 Vol.45 No.7, pp. 435~512
COVER PICTURE
Mesenchymal stem cells (MSCs) are multipotent stem cells capable of differentiating into mesodermal lineages like adipogenic, osteogenic, and chondrogenic. Alcian blue-positive extracellular matrix secreted by chondrocytes in the lacuna confirmed the chondrogenic differentiation of MSCs (Bashyal et al., pp. 479-494).

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