3G4H

Crystal structure of Human Senescence Marker Protein-30 (Zinc Bound)

Summary for 3G4H

• Entry DOI: 10.2210/pdb3g4h/pdb
• Related: 3G4E
• Descriptor: Regucalcin, ZINC ION (3 entities in total)
• Functional Keywords: six bladed beta propeller, gluconolactonase, organophosphate hydrolase, regucalcin, zinc bound, alternative splicing, calcium, cytoplasm, phosphoprotein, signaling protein, hydrolase
• Biological source: Homo sapiens (Human)
• Cellular location: Cytoplasm (By similarity): Q15493
• Total number of polymer chains: 2
• Total formula weight: 66277.79

Authors

Chakraborti, S.,Bahnson, B.J. (deposition date: 2009-02-03, release date: 2010-02-02, Last modification date: 2023-09-06)

Primary citation

Chakraborti, S.,Bahnson, B.J.
Crystal structure of human senescence marker protein 30: insights linking structural, enzymatic, and physiological functions .
Biochemistry, 49:3436-3444, 2010

PubMed Abstract: Human senescence marker protein 30 (SMP30), which functions enzymatically as a lactonase, hydrolyzes various carbohydrate lactones. The penultimate step in vitamin-C biosynthesis is catalyzed by this enzyme in nonprimate mammals. It has also been implicated as an organophosphate hydrolase, with the ability to hydrolyze diisopropyl phosphofluoridate and other nerve agents. SMP30 was originally identified as an aging marker protein, whose expression decreased androgen independently in aging cells. SMP30 is also referred to as regucalcin and has been suggested to have functions in calcium homeostasis. The crystal structure of the human enzyme has been solved from X-ray diffraction data collected to a resolution of 1.4 A. The protein has a 6-bladed beta-propeller fold, and it contains a single metal ion. Crystal structures have been solved with the metal site bound with either a Ca(2+) or a Zn(2+) atom. The catalytic role of the metal ion has been confirmed by mutagenesis of the metal coordinating residues. Kinetic studies using the substrate gluconolactone showed a k(cat) preference of divalent cations in the order Zn(2+) > Mn(2+) > Ca(2+) > Mg(2+). Notably, the Ca(2+) had a significantly higher value of K(d) compared to those of the other metal ions tested (566, 82, 7, and 0.6 mum for Ca(2+), Mg(2+), Zn(2+), and Mn(2+), respectively), suggesting that the Ca(2+)-bound form may be physiologically relevant for stressed cells with an elevated free calcium level.

PubMed: 20329768
DOI: 10.1021/bi9022297

Experimental method

X-RAY DIFFRACTION (1.92 Å)