Journal:Acta Cryst F:S2053230X18016217

The structure of Mycobacterium tuberculosis HtrA reveals an auto-regulatory mechanism

Arvind Kumar Gupta, Debashree Behera and Balasubramanian Gopal ^[1]

Molecular Tour
There are three HtrA paralogues in M. tuberculosis viz., HtrA (Rv1223), PepD (Rv0983) and PepA (Rv0125). Among these, only HtrA is essential for bacterial survival. M. tuberculosis PepD participates in a two component signaling pathway involving MprAB and σ^E. It has been suggested that recognition of misfolded proteins by the PDZ domain in PepD activates this pathway. However, unlike DegS, this HtrA homologue is constitutively active and the PDZ domain positively modulates its enzymatic activity. An aspect that is less explored in this context is the role of the N-terminal cytoplasmic domain. Both HtrA and PepD are predicted to have a cytoplasmic polypeptide stretch of 100-150 residues.

A common structural feature of HtrA proteases is that of a trypsin-like serine protease domain attached to one or more PDZ domains. An in silico analysis of the topological arrangement of these proteases suggests that they are likely to adopt a similar N_in-C_out conformation with one transmembrane helix. Given substantial sequence and structural conservation, the precise roles as well as the rationale for multiple HtrA paralogues in a bacterium are difficult to predict. This aspect is of particular significance to M. tuberculosis as HtrA enzymes govern virulence but the molecular details remain unclear.

The crystal structure of M. tuberculosis HtrA (ΔTM HtrA) that was determined at 1.83 Å resolution. We note that this enzyme exhibits both monomeric as well as trimeric forms in solution. The structure reveals a conformation that would require minor structural alterations for proteolytic activity. Structural features thus suggest that M. tuberculosis HtrA is a regulated protease as opposed to the two other paralogues, PepD and PepA. This essential enzyme is thus likely to be involved in specific signal transduction role as opposed to housekeeping in the recognition and degradation of partially folded or misfolded proteins.

The was determined at a resolution of 1.83Å (PDB ID: 6ieo). In this crystal form, there is one molecule of HtrA in the asymmetric unit. The structure of the periplasmic domain reveals one (226-436; colored in royalblue) flexibly tethered to the (443-528; in gold) at the C-terminal end. The (Alpha Helices, Beta Strands ,  Loops , Turns) referred to as the N-terminal and C-terminal β-barrel. While the N-terminal β-barrel contains the active site residues His270 and Asp306, the C-terminal β-barrel has Ser387 from (colored in yellow). The substantial structural conservation across HtrA enzymes suggests a similar reaction mechanism as evident from the positive charge cavity (the oxyanion hole) which helps in stabilization of tetrahedral intermediate during the acylation step of catalysis. The side chain of the active site serine, Ser387, could be modelled in two alternate conformations with an occupancy of 0.53 and 0.47. Of note, that N_δ1 (His270) and O_δ1/O_δ2 (Asp306) are within (2.6Å /3.2Å). On the other hand, the orientation of active site histidine places N_ε2 of His270 from the O_ϒ of Ser387. The orientation of H270 (N_ε2) and Ser387 (O_γ) (separated by ca 8.0Å) suggests that this crystal structure represents an inactive conformation. The PDZ domain is linked to the protease domain by a . Based on extensive analysis of E. coli DegS, the L1 and L3 loops are essential for regulation of protease activity whereas the L2 loop governs substrate specificity.^[2] (loops are in green, active site residues are in yellow). These loops connecting helices or strands in protease domain. The movement of L3 loop away from PDZ domain has been shown to shift the equilibrium from the inactive to active state of DegS upon peptide binding to PDZ domain.^[3] In the M. tuberculosis HtrA structure, was noted that the L3 loop is displaced from the PDZ domain.

(M. tuberculosis HtrA active site residues are in yellow). The active site residues from bovine trypsin and proteases belonging to the HtrA family from different species were superposed with M. tuberculosis ΔTM HtrA. Two well characterized HtrA proteases (M. tuberculosis PepD (PDB ID: 2z9i; colored in salmon), E. coli DegS (PDB ID: 1soz; colored in cyan)) provided a basis for this comparison alongside bovine trypsin structures. Among these, one is a complex with phenylmethylsulfonyl fluoride (PMSF) (PDB ID: 1pqa; colored in dodgerblue) providing a reference for a covalently linked ligand to active site Ser-OH. The other representative model for a substrate bound form is the trypsin-peptide complex (AAPK) (PDB ID: 2agg; colored in violet). This structure provides a representation of the oxyanion hole wherein the peptide is bound to the active site Ser-OH providing a structural snapshot of the acyl enzyme intermediate. In both examples, the active site Histidine is flipped with χ¹ of 80.7° and -166.8° in the case of peptide bound (1pqa) or 89.4° and -174.8° in the case of the PMSF complex (2agg).^[4][5] For comparison, the Histidine rotamers with χ¹ of 80.7° and 89.4° represent the canonical catalytic triad alongside the active site Asp and Ser. Of note, that the χ¹ of His270 of M. tuberculosis HtrA is -80.9 leading a distorted catalytic triad. This conformation of the catalytic triad in M. tuberculosis HtrA thus represents either an inactive state or a distorted conformation mimicking Histidine flipping in the acylation step of catalysis.

PDB reference: M. tuberculosis HtrA, 6ieo.

References

1. ↑ Gupta AK, Behera D, Gopal B. The crystal structure of Mycobacterium tuberculosis high-temperature requirement A protein reveals an autoregulatory mechanism. Acta Crystallogr F Struct Biol Commun. 2018 Dec 1;74(Pt 12):803-809. doi:, 10.1107/S2053230X18016217. Epub 2018 Nov 29. PMID:30511675 doi:http://dx.doi.org/10.1107/S2053230X18016217
2. ↑ Hasenbein S, Meltzer M, Hauske P, Kaiser M, Huber R, Clausen T, Ehrmann M. Conversion of a regulatory into a degradative protease. J Mol Biol. 2010 Apr 9;397(4):957-66. doi: 10.1016/j.jmb.2010.02.027. Epub 2010, Feb 22. PMID:20184896 doi:http://dx.doi.org/10.1016/j.jmb.2010.02.027
3. ↑ Sohn J, Grant RA, Sauer RT. OMP peptides activate the DegS stress-sensor protease by a relief of inhibition mechanism. Structure. 2009 Oct 14;17(10):1411-21. PMID:19836340 doi:10.1016/j.str.2009.07.017
4. ↑ Ash EL, Sudmeier JL, Day RM, Vincent M, Torchilin EV, Haddad KC, Bradshaw EM, Sanford DG, Bachovchin WW. Unusual 1H NMR chemical shifts support (His) C(epsilon) 1...O==C H-bond: proposal for reaction-driven ring flip mechanism in serine protease catalysis. Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10371-6. PMID:10984533
5. ↑ Radisky ES, Lee JM, Lu CJ, Koshland DE Jr. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates. Proc Natl Acad Sci U S A. 2006 May 2;103(18):6835-40. Epub 2006 Apr 24. PMID:16636277