1UJ5

Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase complexed with ribose-5-phosphate

Summary for 1UJ5

• Entry DOI: 10.2210/pdb1uj5/pdb
• Related: 1UJ4 1UJ6
• Descriptor: ribose 5-phosphate isomerase, RIBULOSE-5-PHOSPHATE, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: enzyme-substrate complex, riken structural genomics/proteomics initiative, rsgi, structural genomics, isomerase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 1
• Total formula weight: 24396.94

Authors

Hamada, K.,Ago, H.,Sugahara, M.,Nodake, Y.,Kuramitsu, S.,Yokoyama, S.,Miyano, M.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2003-07-26, release date: 2004-07-13, Last modification date: 2023-12-27)

Primary citation

Hamada, K.,Ago, H.,Sugahara, M.,Nodake, Y.,Kuramitsu, S.,Miyano, M.
Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi)
J.Biol.Chem., 278:49183-49190, 2003

PubMed Abstract: Ribose-5-phosphate isomerase (Rpi) acts as a key enzyme in the oxidative and reductive pentose-phosphate pathways for the conversion of ribose-5-phosphate (R5P) to ribulose-5-phosphate and vice versa. We have determined the crystal structures of Rpi from Thermus thermophilus HB8 in complex with the open chain form of the substrate R5P and the open chain form of the C2 epimeric inhibitor arabinose-5-phosphate as well as the apo form at high resolution. The crystal structures of both complexes revealed that these ring-opened epimers are bound in the active site in a mirror symmetry binding mode. The O1 atoms are stabilized by an oxyanion hole composed of the backbone amide nitrogens in the conserved motif. In the structure of the Rpi.R5P complex, the conversion moiety O1-C1-C2-O2 in cis-configuration interacts with the carboxyl oxygens of Glu-108 in a water-excluded environment. Furthermore, the C2 hydroxyl group is presumed to be highly polarized by short hydrogen bonding with the side chain of Lys-99. R5P bound as the ring-opened reaction intermediate clarified the high stereoselectivity of the catalysis and is consistent with an aldose-ketose conversion by Rpi that proceeds via a cis-enediolate intermediate.

PubMed: 13679361
DOI: 10.1074/jbc.M309272200

Experimental method

X-RAY DIFFRACTION (2 Å)