Datasets, processing and refinement details for Mtb -AnPRT: inhibitor structures with various space groups

Abstract

There are twenty-five published structures of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (Mtb-AnPRT) that use the same crystallization protocol. The structures include protein complexed with natural and alternative substrates, protein:inhibitor complexes, and variants with mutations of substrate-binding residues. Amongst these are varying space groups (i.e. P21, C2, P21212, P212121). This article outlines experimental details for 3 additional Mtb-AnPRT:inhibitor structures. For one protein:inhibitor complex, two datasets are presented – one generated by crystallization of protein in the presence of the inhibitor and another where a protein crystal was soaked with the inhibitor. Automatic and manual processing of these datasets indicated the same space group for both datasets and thus indicate that the space group differences between structures of Mtb-AnPRT:ligand complexes are not related to the method used to introduce the ligand.

Inhibition and reaction mechanism of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase: A potential target for novel drug design

“…The superpositions of the P1211 and C121 structures indicate that the lattice in the P1211 structure corresponds to an intermediate position between the lattice observed for the C121 structures. 68 This also supports the hypothesis that the subunits that are related by crystallographic symmetry elements in the C121 or P212121 structures are related by pseudosymmetry elements in the P1211 structure. Pseudosymmetry occurs where a noncrystallographic symmetry element within the asymmetric unit is close to a crystallographic symmetry operator.…”

“…The overall conformation of the PRPP binding site is similar in different structures of P. carotovorum AnPRT (PDB: 1KGZ), 56 S. solfataricus AnPRT (PDB: 1ZXY), 67 T. thermophilus AnPRT (PDB: 1VG8) and over 28 published structures of M. tuberculosis. 53,54,57,60,66,68,69 The M. tuberculosis AnPRT structure (PDB: 1ZVW) contains PRPP coordinated in an "extended" form between the β1-α5 and β2-α6 loops, with the diphosphate group buried the most deeply (Figure 1.9, A). and S. solfataricus 1ZXY structures but PRPP accommodates itself into an "S"-shaped arrangement in the S. solfataricus 1ZXY structure.…”

“…Crystal structures of M. tuberculosis AnPRT complexed with these phosphonate inhibitors were solved to shed light on the binding of these inhibitors as well as to investigate the extent to which the phosphonate moiety could reach into the PRPP binding site of the enzyme. The crystal structure of M. tuberculosis AnPRT in complex with a bianthranilate phosphonate inhibitor was obtained using the soaking method published by Evan et al 68 As soaked inhibitors may cause conformational changes in the protein leading to disruption in crystal contacts, phosphonate inhibitors were co-crystallised successfully with M. tuberculosis AnPRT enzyme. These structures allow us to interpret the differences that occurred in the enzyme by introducing the inhibitor using either a ligand soaking or co-crystallisation method.…”

“…tuberculosis AnPRT were already solved by Dr G. L. Evans at the School of Biological Sciences, University of Auckland. 54,68 These inhibitor-bound crystals were grown using inhibitor soaking or streak-seeding using wild-type AnPRT. Hence, these three structures complement the information found via enzymology in this study and provide a comparison to the five new structures complexed with the phosphonate ligands obtained by the co-crystallisation method, in the presence or absence of the PRPP substrate.…”

“…The structure of M. tuberculosis AnPRT was obtained in complex with ligand 2.6 and solved in the space group P212121, the most common space group for this protein. 68 Two monomeric units were present in the asymmetric unit. Both monomers have a similar binding mode for phosphonate inhibitor 2.6 in which aromatic rings moiety of 2.6 bind between sites 2 and 3 (site 2-3) within substrate binding tunnel ( showing the density into which ligand 2.6 was modelled.…”