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Title3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 10538, Year 2024
Publish dateDec 3, 2024
AuthorsAdriana Coricello / Alanya J Nardone / Antonio Lupia / Carmen Gratteri / Matthijn Vos / Vincent Chaptal / Stefano Alcaro / Wen Zhu / Yuichiro Takagi / Nigel G J Richards /
PubMed AbstractAdvances 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 ...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.
External linksNat Commun / PubMed:39627226 / PubMed Central
MethodsEM (single particle)
Resolution3.35 - 3.5 Å
Structure data

40764

8sue

EMDB-40764, PDB-8sue:
Human asparagine synthetase (apo-ASNS)
Method: EM (single particle) / Resolution: 3.5 Å

44253

9b6c

EMDB-44253, PDB-9b6c:
Human asparagine synthetase Arg-142 to Ile-142 (R142I) variant
Method: EM (single particle) / Resolution: 3.35 Å

Source
  • homo sapiens (human)
KeywordsBIOSYNTHETIC PROTEIN / asparagine / aspartic acid / glutamine / ammonia

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