PDBsum entry 1js1

Transferase

PDB id: 1js1

Contents

Protein chains

324 a.a. *

Ligands

PO4 ×3

Waters ×422

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of a transcarbamylase-Like protein from the anaerobic bacterium bacteroides fragilis at 2.0 a resolution.

Authors

D.Shi, R.Gallegos, J.Deponte, H.Morizono, X.Yu, N.M.Allewell, M.Malamy, M.Tuchman.

Ref.

J Mol Biol, 2002, 320, 899-908. [DOI no: 10.1016/S0022-2836(02)00539-9]

PubMed id

12095263

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.

Figure 1.
Figure 1. Ribbon diagram of the monomer. Green arrows indicate segments that are hydrogen bonded to an adjacent strand as required by the Kabsch & Sander[38] definition of b character. a-Helices are light blue and 3[10] helices are dark blue. The phosphate group is represented as a ball-and-stick model. The Figure was drawn with RIBBONS.[39]

Figure 4.
Figure 4. Comparison of the carbamoyl phosphate binding site between the B. fragilis transcarbamylase-like structure and human OTCase. (a) Putative carbamoyl phosphate-binding site in the B. fragilis protein. The phosphate group and two active-site water molecules are shown as a ball-and-stick model. (b) Carbamoyl phosphate-binding site in human OTCase.[42] CP is shown as a thick ball-and-stick model. The phosphate group in the B. fragilis protein is located in the same position as the phosphate moiety of CP in human OTCase and interacts with the protein in a similar way. Two water molecules occupy the respective positions of the carbamoyl nitrogen and oxygen atoms of CP. The Figure was drawn with MOLSCRIPT.[41]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 899-908) copyright 2002.