6qhv

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Time resolved structural analysis of the full turnover of an enzyme - 100 ms

Structural highlights

6qhv is a 2 chain structure with sequence from Rhodopseudomonas palustris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.715Å
Ligands:FAH
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DEHA_RHOPA Catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. Has lower activity towards bromoacetate and chloroacetate.[1] [2]

Publication Abstract from PubMed

A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework's dynamics and entropy constitute crucial components of the catalytic machinery.

Time-resolved crystallography reveals allosteric communication aligned with molecular breathing.,Mehrabi P, Schulz EC, Dsouza R, Muller-Werkmeister HM, Tellkamp F, Miller RJD, Pai EF Science. 2019 Sep 13;365(6458):1167-1170. doi: 10.1126/science.aaw9904. PMID:31515393[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
6 reviews cite this structure
Moving beyond static snapshots: Protein dynamics and the Protein Data Bank.
Miller et al. (2021)
5 more
30 other articles
No citations found

See Also

References

  1. ↑ Chan PW, Yakunin AF, Edwards EA, Pai EF. Mapping the Reaction Coordinates of Enzymatic Defluorination. J Am Chem Soc. 2011 Apr 21. PMID:21510690 doi:10.1021/ja200277d
  2. ↑ Chan PW, Yakunin AF, Edwards EA, Pai EF. Mapping the Reaction Coordinates of Enzymatic Defluorination. J Am Chem Soc. 2011 Apr 21. PMID:21510690 doi:10.1021/ja200277d
  3. ↑ Mehrabi P, Schulz EC, Dsouza R, Müller-Werkmeister HM, Tellkamp F, Miller RJD, Pai EF. Time-resolved crystallography reveals allosteric communication aligned with molecular breathing. Science. 2019 Sep 13;365(6458):1167-1170. PMID:31515393 doi:10.1126/science.aaw9904

Contents


PDB ID 6qhv

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