2E67

Crystal structure of the hypothetical protein TTHB029 from Thermus thermophilus HB8

Summary for 2E67

• Entry DOI: 10.2210/pdb2e67/pdb
• Descriptor: Hypothetical protein TTHB029, MAGNESIUM ION (3 entities in total)
• Functional Keywords: hypothetical protein, nppsfa, national project on protein structural and functional analyses, structural genomics, unknown function, riken structural genomics/proteomics initiative, rsgi
• Biological source: Thermus thermophilus
• Total number of polymer chains: 6
• Total formula weight: 177955.07

Authors

Imagawa, T.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2006-12-26, release date: 2007-06-26, Last modification date: 2024-03-13)

Primary citation

Imagawa, T.,Iino, H.,Kanagawa, M.,Ebihara, A.,Kuramitsu, S.,Tsuge, H.
Crystal structure of the YdjC-family protein TTHB029 from Thermus thermophilus HB8: structural relationship with peptidoglycan N-acetylglucosamine deacetylase.
Biochem.Biophys.Res.Commun., 367:535-541, 2008

PubMed Abstract: 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.

PubMed: 18177738
DOI: 10.1016/j.bbrc.2007.12.144

Experimental method

X-RAY DIFFRACTION (2.9 Å)