1JS1

Crystal Structure of a new transcarbamylase from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution

Summary for 1JS1

• Entry DOI: 10.2210/pdb1js1/pdb
• Descriptor: Transcarbamylase, PHOSPHATE ION (3 entities in total)
• Functional Keywords: alpha/beta topology, two domains, transferase
• Biological source: Bacteroides fragilis
• Cellular location: Cytoplasm : Q8A1E9
• Total number of polymer chains: 3
• Total formula weight: 112111.46

Authors

Shi, D.,Gallegos, R.,DePonte III, J.,Morizono, H.,Yu, X.,Allewell, N.M.,Malamy, M.,Tuchman, M. (deposition date: 2001-08-15, release date: 2002-07-17, Last modification date: 2024-02-07)

Primary citation

Shi, D.,Gallegos, R.,DePonte III, J.,Morizono, H.,Yu, X.,Allewell, N.M.,Malamy, M.,Tuchman, M.
Crystal structure of a transcarbamylase-like protein from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution.
J.Mol.Biol., 320:899-908, 2002

PubMed Abstract: A transcarbamylase-like protein essential for arginine biosynthesis in the anaerobic bacterium Bacteroides fragilis has been purified and crystallized in space group P4(3)2(1)2 (a=b=153.4 A, c=94.8 A). The structure was solved using a single isomorphous replacement with anomalous scattering (SIRAS) and was refined at 2.0 A resolution to an R-factor of 20.6% (R-free=25.2%). The molecular model is trimeric and comprises 960 amino acid residues, two phosphate groups and 422 water molecules. The monomer has the consensus transcarbamylase fold with two structural domains linked by two long interdomain helices: the putative carbamoyl phosphate-binding domain and a binding domain for the second substrate. Each domain has a central parallel beta-sheet surrounded by alpha-helices and loops with alpha/beta topology. The putative carbamoyl phosphate-binding site is similar to those in ornithine transcarbamylases (OTCases) and aspartate transcarbamylases (ATCases); however, the second substrate-binding site is strikingly different. This site has several insertions and deletions, and residues critical to substrate binding and catalysis in other known transcarbamylases are not conserved. The three-dimensional structure and the fact that this protein is essential for arginine biosynthesis suggest strongly that it is a new member of the transcarbamylase family. A similar protein has been found in Xylella fastidiosa, a bacterium that infects grapes, citrus and other plants.

PubMed: 12095263
DOI: 10.1016/S0022-2836(02)00539-9

Experimental method

X-RAY DIFFRACTION (2 Å)