3RPM

Crystal structure of the first GH20 domain of a novel Beta-N-acetyl-hexosaminidase StrH from Streptococcus pneumoniae R6

Summary for 3RPM

• Entry DOI: 10.2210/pdb3rpm/pdb
• Descriptor: Beta-N-acetyl-hexosaminidase, 2-acetamido-2-deoxy-beta-D-glucopyranose, PENTAETHYLENE GLYCOL, ... (4 entities in total)
• Functional Keywords: tim barrel, beta-n-acetyl-hexosaminidase, hydrolase
• Biological source: Streptococcus pneumoniae
• Cellular location: Secreted, cell wall; Peptidoglycan-anchor (By similarity): Q8DRL6
• Total number of polymer chains: 2
• Total formula weight: 105334.82

Authors

Jiang, Y.L.,Yu, W.L.,Zhang, J.W. (deposition date: 2011-04-27, release date: 2011-10-26, Last modification date: 2024-11-20)

Primary citation

Jiang, Y.L.,Yu, W.L.,Zhang, J.W.,Frolet, C.,Di Guilmi, A.-M.,Zhou, C.Z.,Vernet, T.,Chen, Y.
Structural basis for the substrate specificity of a novel beta-N-acetylhexosaminidase StrH protein from Streptococcus pneumoniae R6
J.Biol.Chem., 286:43004-43012, 2011

PubMed Abstract: The β-N-acetylhexosaminidase (EC 3.2.1.52) from glycoside hydrolase family 20 (GH20) catalyzes the hydrolysis of the β-N-acetylglucosamine (NAG) group from the nonreducing end of various glycoconjugates. The putative surface-exposed N-acetylhexosaminidase StrH/Spr0057 from Streptococcus pneumoniae R6 was proved to contribute to the virulence by removal of β(1,2)-linked NAG on host defense molecules following the cleavage of sialic acid and galactose by neuraminidase and β-galactosidase, respectively. StrH is the only reported GH20 enzyme that contains a tandem repeat of two 53% sequence-identical catalytic domains (designated as GH20-1 and GH20-2, respectively). Here, we present the 2.1 Å crystal structure of the N-terminal domain of StrH (residues Glu-175 to Lys-642) complexed with NAG. It adopts an overall structure similar to other GH20 enzymes: a (β/α)(8) TIM barrel with the active site residing at the center of the β-barrel convex side. The kinetic investigation using 4-nitrophenyl N-acetyl-β-d-glucosaminide as the substrate demonstrated that GH20-1 had an enzymatic activity (k(cat)/K(m)) of one-fourth compared with GH20-2. The lower activity of GH20-1 could be attributed to the substitution of active site Cys-469 of GH20-1 to the counterpart Tyr-903 of GH20-2. A complex model of NAGβ(1,2)Man at the active site of GH20-1 combined with activity assays of the corresponding site-directed mutants characterized two key residues Trp-443 and Tyr-482 at subsite +1 of GH20-1 (Trp-876 and Tyr-914 of GH20-2) that might determine the β(1,2) substrate specificity. Taken together, these findings shed light on the mechanism of catalytic specificity toward the β(1,2)-linked β-N-acetylglucosides.

PubMed: 22013074
DOI: 10.1074/jbc.M111.256578

Experimental method

X-RAY DIFFRACTION (2.1 Å)