Functional and structural characterization of ovine ornithine transcarbamoylaseElectronic supplementary information (ESI) available: a Ramachandran plot, and two figures illustrating statistics on the geometrical parameters of the structure. See http://www.rsc.org/suppdata/ob/b3/b304901a/

Abstract

Ornithine transcarbamoylase from ovine liver has been purified to homogeneity. Like all anabolic OTCs, the ovine enzyme is a trimer, constituted by identical subunits of 34 kDa. Sequence analysis of the 54 N-terminal residues of ovine OTC shows a high degree of homology with the human enzyme. The optimum pH and the Michaelis constants for the catalytic reaction were determined. The ovine enzyme is the most thermostable one among mammals OTCs, its critical temperature being 6 degrees C higher than those measured for the other enzymes. The enzyme has been crystallised and the structure determined at 3.5 A resolution. Crystals belong to the cubic P4(3)32 space group, with a = b = c = 184.7 A and a solvent content of about 80%. There is no evidence of any ligand in the active site cavity, indicating that the crystals contain an unliganded or T state of the enzyme. The unliganded OTCase enzyme adopts a trimeric structure which, in the crystal, presents a three-fold axis coincident with the crystallographic one. The conformation of each monomer in the trimer is quite similar to that of the liganded human protein, with the exception of a few loops, directly interacting with the substrate(s), which are able to induce a rearrangement of the quaternary organisation of the trimer, that accounts for the cooperative behaviour of the enzyme following the binding of the substrates.

Structure of anabolic ornithine carbamoyltransferase fromCampylobacter jejuniat 2.7 Å resolution

“…The side chain of this glutamine or histidine participates in substrate binding via a hydrogen bond to the phosphate moiety of CP, anchoring the loop in a similar conformation in all OTC structures that contain this ligand. The unliganded OTC structures demonstrate a variety of B2-H3 loop conformations, which is consistent with ordering of this loop upon CP binding (De Gregorio et al, 2003). In the Cje aOTC structure this loop is disordered and most of the side chains could not be modeled in the electron-density map.…”

“…Even the main-chain atoms of residues 74-76 are not modeled in subunit F. The conformation of the B2-H3 loop is similar in all of the other Cje OTC subunits and is different from the conformation of the loop in CP-complexed OTCs (Fig. 5), with the displacement of Gln73 C being about 6 Å (Shi et al, 2000;De Gregorio et al, 2003). Superposition of Cje aOTC subunit D (green) and human aOTC (yellow; PDB entry 1c9y) in two different orientations.…”

From Genome to Structure and Back Again: A Family Portrait of the Transcarbamylases

“…However, the OTCase from the thermophilic T. thermophilus appears to be a trimer. Among mammals, four OTCase structures from humans [ 21 , 58 , 59 , 60 ] and one from sheep [ 61 ], have been determined.…”

Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae

“…The right panel shows a schematic representation of the sequence alignment; scales indicate the position of the alignment. The references of the entries used in the analysis: 1A1S ( Villeret et al., 1998 ), 1ACM ( Stebbins et al., 1992 ), 1C9Y ( Shi et al., 2000 ), 1DUV ( Langley et al., 2000 ), 1DXH, 1FB5 ( De Gregorio et al., 2003 ), 1JS1 ( Shi et al., 2002 ), 1ML4 ( Van Boxstael et al., 2003 ), 1PG5 ( De Vos et al., 2004 ), 1VLV, 2AT2 ( Stevens et al., 1991 ), 2BE7 ( De Vos et al., 2007 ), 2EF0, 2G7M ( Shi et al., 2007 ), 2I6U ( Sankaranarayanan et al., 2008 ), 2RGW ( Vitali et al., 2008 ), 2W37 ( de las Rivas et al., 2009 ), 3D6N ( Zhang et al., 2009 ), 3GRF ( Galkin et al., 2009 ), 3KZC ( Shi et al., 2005 ), 3Q98 ( Li et al., 2011 ), 3SDS ( Hewitt et al., 2011 ), 3TPF ( Shabalin et al., 2012 ), 4AMU ( Gallego et al., 2012 ), 4F2G ( Baugh et al., 2013 ), 5ILQ ( Lunev et al., 2016 ), 6YPO ( Bellin et al., 2021 ), 8QEU (this work).…”