Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center

Takayuki Ohnuma, Naoyuki Umemoto, Takuya Nagata, Shoko Shinya, Tomoyuki Numata, Toki Taira, Tamo Fukamizo

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Descriptions The structure of a GH19 chitinase from the moss Bryum coronatum (BcChi-A) in complex with the substrate was examined by X-ray crystallography and NMR spectroscopy in solution. The X-ray crystal structure of the inactive mutant of BcChi-A (BcChi-A-E61A) liganded with chitin tetramer (GlcNAc)4 revealed a clear electron density of the tetramer bound to subsites - 2, - 1, + 1, and + 2. Individual sugar residues were recognized by several amino acids at these subsites through a number of hydrogen bonds. This is the first crystal structure of GH19 chitinase liganded with oligosaccharide spanning the catalytic center. NMR titration experiments of chitin oligosaccharides into the BcChi-A-E61A solution showed that the binding mode observed in the crystal structure is similar to that in solution. The C-1 carbon of - 1 GlcNAc, the Oε1 atom of the catalytic base (Glu70), and the Oγ atom of Ser102 form a "triangle" surrounding the catalytic water, and the arrangement structurally validated the proposed catalytic mechanism of GH19 chitinases. The glycosidic linkage between - 1 and + 1 sugars was found to be twisted and under strain. This situation may contribute to the reduction of activation energy for hydrolysis. The complex structure revealed a more refined mechanism of the chitinase catalysis.

Original languageEnglish
Pages (from-to)793-802
Number of pages10
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Volume1844
Issue number4
DOIs
Publication statusPublished - Apr 2014
Externally publishedYes

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Chitinases
Chitin
Crystal structure
Oligosaccharides
Sugars
Bryophyta
Atoms
X ray crystallography
X Ray Crystallography
Catalysis
Titration
Nuclear magnetic resonance spectroscopy
Carrier concentration
Hydrogen
Hydrolysis
Hydrogen bonds
Magnetic Resonance Spectroscopy
Carbon
Activation energy
Nuclear magnetic resonance

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry
  • Biophysics
  • Biochemistry
  • Molecular Biology

Cite this

Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center. / Ohnuma, Takayuki; Umemoto, Naoyuki; Nagata, Takuya; Shinya, Shoko; Numata, Tomoyuki; Taira, Toki; Fukamizo, Tamo.

In: Biochimica et Biophysica Acta - Proteins and Proteomics, Vol. 1844, No. 4, 04.2014, p. 793-802.

Research output: Contribution to journalArticle

Ohnuma, Takayuki ; Umemoto, Naoyuki ; Nagata, Takuya ; Shinya, Shoko ; Numata, Tomoyuki ; Taira, Toki ; Fukamizo, Tamo. / Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center. In: Biochimica et Biophysica Acta - Proteins and Proteomics. 2014 ; Vol. 1844, No. 4. pp. 793-802.
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