Crystal structure of the YdjC-family protein TTHB029 from Thermus thermophilus HB8: structural relationship with peptidoglycan N-acetylglucosamine deacetylase.
The YdjC-family protein is widely distributed, from human to bacteria, but so far no three-dimensional structure and functional analysis of this family of proteins has been reported. We determined the three-dimensional structure of the YdjC homolog TTHB029 at a resolution of 2.9A. The overall structure of the monomer consists of (betaalpha)-barrel fold forming a homodimer. Asp21, His60, and His127 residues coordinate to Mg(2+) as a possible active site. TTHB029 shows structural similarity to the peptidoglycan N-acetylglucosamine deacetylase from Streptococcus pneumoniae (SpPgdA). The active site groove of SpPgdA includes the Zn(2+) coordinated to Asp276, His326, and His330. Despite the low sequence identity, metal-binding residues of Asp-His-His were conserved among the two enzymes. There were definitive differences, however, in that one of the histidines of the metal-binding site was substituted for the other histidine located on the other loop. Moreover, these important metal-binding residues and the residues of the presumed active site are fully conserved in YdjC-family protein.
Imagawa
Takahito
T
Institute for Health Sciences, Tokushima Bunri University, 180 Nishihama, Yamashiro, Tokushima 770-8514, Japan.
Iino
Hitoshi
H
Kanagawa
Mayumi
M
Ebihara
Akio
A
Kuramitsu
Seiki
S
Tsuge
Hideaki
H
D000581:Amidohydrolases / Q000737:chemistry*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D013293:Enterococcus faecalis / Q000201:enzymology; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013296:Streptococcus pneumoniae / Q000201:enzymology; D016963:Thermus thermophilus / Q000737:chemistry*
D001426:Bacterial Proteins; D000581:Amidohydrolases; C411846:pgdA protein, Streptococcus pneumoniae