4GNB

human SMP30/GNL

Summary for 4GNB

• Entry DOI: 10.2210/pdb4gnb/pdb
• Related: 4GN7 4GN8 4GN9 4GNA 4GNC
• Descriptor: Regucalcin, CALCIUM ION (3 entities in total)
• Functional Keywords: beta propeller structure, hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm (By similarity): Q15493
• Total number of polymer chains: 2
• Total formula weight: 66703.76

Authors

Aizawa, S.,Senda, M.,Harada, A.,Maruyama, N.,Ishida, T.,Aigaki, T.,Ishigami, A.,Senda, T. (deposition date: 2012-08-17, release date: 2013-04-10, Last modification date: 2023-11-08)

Primary citation

Aizawa, S.,Senda, M.,Harada, A.,Maruyama, N.,Ishida, T.,Aigaki, T.,Ishigami, A.,Senda, T.
Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase
Plos One, 8:e53706-e53706, 2013

PubMed Abstract: The senescence marker protein-30 (SMP30), which is also called regucalcin, exhibits gluconolactonase (GNL) activity. Biochemical and biological analyses revealed that SMP30/GNL catalyzes formation of the γ-lactone-ring of L-gulonate in the ascorbic acid biosynthesis pathway. The molecular basis of the γ-lactone formation, however, remains elusive due to the lack of structural information on SMP30/GNL in complex with its substrate. Here, we report the crystal structures of mouse SMP30/GNL and its complex with xylitol, a substrate analogue, and those with 1,5-anhydro-D-glucitol and D-glucose, product analogues. Comparison of the crystal structure of mouse SMP30/GNL with other related enzymes has revealed unique characteristics of mouse SMP30/GNL. First, the substrate-binding pocket of mouse SMP30/GNL is designed to specifically recognize monosaccharide molecules. The divalent metal ion in the active site and polar residues lining the substrate-binding cavity interact with hydroxyl groups of substrate/product analogues. Second, in mouse SMP30/GNL, a lid loop covering the substrate-binding cavity seems to hamper the binding of L-gulonate in an extended (or all-trans) conformation; L-gulonate seems to bind to the active site in a folded conformation. In contrast, the substrate-binding cavities of the other related enzymes are open to the solvent and do not have a cover. This structural feature of mouse SMP30/GNL seems to facilitate the γ-lactone-ring formation.

PubMed: 23349732
DOI: 10.1371/journal.pone.0053706

Experimental method

X-RAY DIFFRACTION (1.5 Å)