8SUE

Human asparagine synthetase (apo-ASNS)

Summary for 8SUE

• Entry DOI: 10.2210/pdb8sue/pdb
• EMDB information: 40764
• Descriptor: Asparagine synthetase [glutamine-hydrolyzing] (1 entity in total)
• Functional Keywords: asparagine, aspartic acid, glutamine, ammonia, biosynthetic protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 128649.23

Authors

Coricello, A.,Zhu, W.,Lupia, A.,Gratteri, C.,Vos, M.,Chaptal, V.,Alcaro, S.,Takagi, Y.,Richards, N. (deposition date: 2023-05-12, release date: 2024-05-22, Last modification date: 2025-02-05)

Primary citation

Coricello, A.,Nardone, A.J.,Lupia, A.,Gratteri, C.,Vos, M.,Chaptal, V.,Alcaro, S.,Zhu, W.,Takagi, Y.,Richards, N.G.J.
3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase.
Nat Commun, 15:10538-10538, 2024

PubMed Abstract: Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we show that 3D variability analysis (3DVA) of the cryo-EM map for wild-type (WT) human asparagine synthetase (ASNS) identifies a functional role for the Arg-142 side chain and test this hypothesis experimentally by characterizing the R142I variant in which Arg-142 is replaced by isoleucine. Support for Arg-142 playing a role in the intramolecular translocation of ammonia between the active site of the enzyme is provided by the glutamine-dependent synthetase activity of the R142 variant relative to WT ASNS, and MD simulations provide a possible molecular mechanism for these findings. Combining 3DVA with MD simulations is a generally applicable approach to generate testable hypotheses of how conformational changes in buried side chains might regulate function in enzymes.

PubMed: 39627226
DOI: 10.1038/s41467-024-54912-9

Experimental method

ELECTRON MICROSCOPY (3.5 Å)