5JJG

Structure of magnesium-loaded ALG-2

Summary for 5JJG

• Entry DOI: 10.2210/pdb5jjg/pdb
• Descriptor: Pcalcium-binding protein ALG-2, rogrammed cell death protein 6, MAGNESIUM ION, ISOPROPYL ALCOHOL, ... (4 entities in total)
• Functional Keywords: alg-2, penta-ef-hand protein, calcium binding protein, apoptosis, apoptosis-linked gene 2
• Biological source: Mus musculus (Mouse)
• Cellular location: Endoplasmic reticulum membrane ; Peripheral membrane protein : P12815
• Total number of polymer chains: 1
• Total formula weight: 20203.46

Authors

Tanner, J.J. (deposition date: 2016-04-23, release date: 2016-09-07, Last modification date: 2023-09-27)

Primary citation

Tanner, J.J.,Frey, B.B.,Pemberton, T.,Henzl, M.T.
EF5 Is the High-Affinity Mg(2+) Site in ALG-2.
Biochemistry, 55:5128-5141, 2016

PubMed Abstract: The penta-EF-hand (PEF) protein ALG-2 (apoptosis-linked gene 2) has been implicated in several important physiological processes, including endoplasmic reticulum-Golgi vesicular transport and endosomal biogenesis/transport. ALG-2 was recently shown to harbor a metal ion-binding site with a high affinity for Mg(2+) and a low affinity for Ca(2+). We herein present the X-ray structure of Mg(2+)-bound ALG-2des23(wt). Although the C(α) trace is nearly indistinguishable from that of the Ca(2+)-free protein, the orientation of the C-terminal helix differs in the two structures. Consistent with that observation, replacement of the +x ligand in EF5, D169, with alanine eliminates high-affinity Mg(2+) binding. It also eliminates the low-affinity Ca(2+) site and lowers the affinity of the remaining Ca(2+)-binding sites, EF3 and EF1. The coordination environment in EF5 approaches ideal Mg(2+) octahedral geometry. The ligand array, consisting of three carboxylates (+x, +y, +z), a backbone carbonyl (-y), and two water molecules (-x, -z), may offer a recipe for a high-affinity, high-selectivity Mg(2+)-binding site. Sequence data for other PEF proteins indicate that select calpain large subunits, notably CAPN1 and CAPN8, may also possess a high-affinity Mg(2+)-binding site. In Mg(2+)-bound ALG-2, the carbonyl of F188 and the C-terminal carboxylate of V191 interact with the ε-ammonium group of K137 in the opposing subunit, suggesting that Mg(2+) binding could have an impact on dimerization. Interestingly, EF1 and EF3 are also occupied in the crystal, despite having modest affinity for Mg(2+). The results of a calorimetry-based analysis indicate that their Mg(2+) binding constants are 2 orders of magnitude lower than that determined for EF5.

PubMed: 27541325
DOI: 10.1021/acs.biochem.6b00596

Experimental method

X-RAY DIFFRACTION (1.72 Å)