3ATU

Crystal structure of human Hsp70 NBD in the ADP- and Mg ion-bound state

Summary for 3ATU

• Entry DOI: 10.2210/pdb3atu/pdb
• Related: 2E88 2E8A 3A8Y 3ATV
• Descriptor: Heat shock 70 kDa protein 1A/1B, ADENOSINE-5'-DIPHOSPHATE, PHOSPHATE ION, ... (7 entities in total)
• Functional Keywords: structural genomics, riken structural genomics/proteomics initiative, rsgi, atpase, adp binding, hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: P08107
• Total number of polymer chains: 1
• Total formula weight: 43840.38

Authors

Arakawa, A.,Handa, N.,Shirouzu, M.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2011-01-13, release date: 2011-12-28, Last modification date: 2023-11-01)

Primary citation

Arakawa, A.,Handa, N.,Shirouzu, M.,Yokoyama, S.
Biochemical and structural studies on the high affinity of Hsp70 for ADP.
Protein Sci., 20:1367-1379, 2011

PubMed Abstract: The molecular chaperone 70-kDa heat shock protein (Hsp70) is driven by ATP hydrolysis and ADP-ATP exchange. ADP dissociation from Hsp70 is reportedly slow in the presence of inorganic phosphate (P(i) ). In this study, we investigated the interaction of Hsp70 and its nucleotide-binding domain (NBD) with ADP in detail, by isothermal titration calorimetry measurements and found that Mg(2+) ion dramatically elevates the affinity of Hsp70 for ADP. On the other hand, P(i) increased the affinity in the presence of Mg(2+) ion, but not in its absence. Thus, P(i) enhances the effect of the Mg(2+) ion on the ADP binding. Next, we determined the crystal structures of the ADP-bound NBD with and without Mg(2+) ion. As compared with the Mg(2+) ion-free structure, the ADP- and Mg(2+) ion-bound NBD contains one Mg(2+) ion, which is coordinated with the β-phosphate group of ADP and associates with Asp10, Glu175, and Asp199, through four water molecules. The Mg(2+) ion is also coordinated with one P(i) molecule, which interacts with Lys71, Glu175, and Thr204. In fact, the mutations of Asp10 and Asp199 reduced the affinity of the NBD for ADP, in both the presence and the absence of P(i) . Therefore, the Mg(2+) ion-mediated network, including the P(i) and water molecules, increases the affinity of Hsp70 for ADP, and thus the dissociation of ADP is slow. In ADP-ATP exchange, the slow ADP dissociation might be rate-limiting. However, the nucleotide-exchange factors actually enhance ADP release by disrupting the Mg(2+) ion-mediated network.

PubMed: 21608060
DOI: 10.1002/pro.663

Experimental method

X-RAY DIFFRACTION (1.65 Å)