5YFW

Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMP

Summary for 5YFW

• Entry DOI: 10.2210/pdb5yfw/pdb
• Descriptor: Ribose 1,5-bisphosphate isomerase, 1,5-di-O-phosphono-alpha-D-ribofuranose, ADENOSINE MONOPHOSPHATE, ... (6 entities in total)
• Functional Keywords: isomerase, nmp degradation pathway, ribose-1, 5-bisphosphate, rossmann-like fold
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 3
• Total formula weight: 111573.50

Authors

Gogoi, P.,Kanaujia, S.P. (deposition date: 2017-09-22, release date: 2018-02-14, Last modification date: 2023-11-22)

Primary citation

Gogoi, P.,Kanaujia, S.P.
A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.
Sci Rep, 8:1891-1891, 2018

PubMed Abstract: The homologues of the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B) are assumed to be present in archaea. Likewise, an ORF, PH0208 in Pyrococcus horikoshii OT3 have been proposed to encode one of the homologues of regulatory subunits of eIF2B. However, PH0208 protein also shares sequence similarity with a functionally non-related enzyme, ribose-1,5-bisphosphate isomerase (R15Pi), involved in conversion of ribose-1,5-bisphosphate (R15P) to ribulose-1,5-bisphosphate (RuBP) in an AMP-dependent manner. Herein, we have determined the crystal structure of PH0208 protein in order to decipher its true function. Although structurally similar to the regulatory subunits of eIF2B, the ability to bind R15P and RuBP suggests that PH0208 would function as R15Pi. Additionally, this study for the first time reports the binding sites of AMP and GMP in R15Pi. The AMP binding site in PH0208 protein clarified the role of AMP in providing structural stability to R15Pi. The binding of GMP to the 'AMP binding site' in addition to its own binding site indicates that GMP might also execute a similar function, though with less specificity. Furthermore, we have utilized the resemblance between PH0208 and the regulatory subunits of eIF2B to propose a model for the regulatory mechanism of eIF2B in eukaryotes.

PubMed: 29382938
DOI: 10.1038/s41598-018-20418-w

Experimental method

X-RAY DIFFRACTION (2.35 Å)