Protein-glutamate methylesterase (CheB)

 

Protein-glutamate methyl-esterase, also known as chemotaxis-specific methylesterase, is involved in regulating the signalling activity of bacterial chemotaxis transmembrane receptors through chemical modification of specific glutamate residues. The protein consists of two main domains, an N-terminal regulatory domain and a C-terminal effector domain. Phosphorylation of the N-terminal domain influences the reactivity of the catalytic C-terminus, although the truncated, C-terminus only protein retains full catalytic activity and substrate specificity [PMID:7608974].

The bacterial chemotaxis receptors are dimeric transmembrane proteins with periplasmic ligand-binding domains that detect specific chemoeffector molecules, and cytoplasmic domains that control the activities of intracellular signalling proteins. Like many of the response regulator proteins, it is a multi-domain protein consisting of an N-terminal regulatory domain and a C-terminal effector domain. Regulation of CheB involves both inter- and intramolecular interactions. The bacterial chemotaxis receptors control the activity of the first cytoplasmic component of the signal transduction pathway, the histidine protein kinase, CheA. The autophosphorylation activity of the CheA kinase is influenced by both the ligand occupancy of the receptors and the level of receptor methylation. Bacterial chemotaxis serves as a useful tool/model for the study of molecular strategies of signal transduction.

Methylester hydrolysis depends both on the conformation of the receptor and on phosphorylation of the Protein-glutamate methylesterase regulatory domain. Phosphorylation of the regulatory domain activates the effector function. The methylesterase active site is identified as a cleft at the C-terminal edge of the beta-sheet containing residues SER 164, HIS 190 and ASP 286. The three-dimensional fold, and the arrangement of residues within the catalytic triad distinguishes the CheB methyltransferase from any previously described serine protease or serine hydrolase. The three-dimensional arrangement of the catalytic triad in the CheB methyl transferase is different from that of previously characterised serine hydrolases and serine proteases due to the opposite orientation of the histidine residue - similar orientations are observed in thiol proteases papain and actinidin.

 

Reference Protein and Structure

Sequence
P04042 UniProt (3.1.1.61, 3.5.1.44) IPR008248 (Sequence Homologues) (PDB Homologues)
Biological species
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (Bacteria) Uniprot
PDB
1chd - CHEB METHYLESTERASE DOMAIN (1.75 Å) PDBe PDBsum 1chd
Catalytic CATH Domains
3.40.50.180 CATHdb (see all for 1chd)
Click To Show Structure

Enzyme Reaction (EC:3.1.1.61)

water
CHEBI:15377ChEBI
+
gamma-methyl L-glutamate residue
CHEBI:82795ChEBI
methanol
CHEBI:17790ChEBI
+
L-glutamate residue
CHEBI:29973ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: CheB methylesterase, PME, Chemotaxis-specific methylesterase, Methyl-accepting chemotaxis protein methyl-esterase, Methylesterase CheB, Protein carboxyl methylesterase, Protein methyl-esterase, Protein methylesterase, Protein-L-glutamate-5-O-methyl-ester acylhydrolase,

Enzyme Mechanism

Introduction

The hydrolysis of carboxyl methyl groups and amide groups catalysed by the CheB methylesterase is expected to involve a catalytic mechanism similar to that of the serine proteases and other hydrolases. The active site proposed is consistent with a proton relay mechanism proposed for hydrolysis by a serine nucleophile within a catalytic triad. For the hydrolysis catalysed by CheB, the proposed reaction mechanism would involve the hydroxyl group of Ser 164 as the nucleophile and the imidazole ring of His 190 as the proton donor to the leaving group, methanol. A potential oxyanion hole for stabilisation of the tetrahedral intermediate would be provided by the backbone amide groups of Met 283 and Thr165.

Catalytic Residues Roles

UniProt PDB* (1chd)
Asp286 Asp286(140)A The residue hydrogen bonds to the (E)N of the His190 imidazole ring, directing and stabilising the catalytic general base within the active site. hydrogen bond acceptor, electrostatic stabiliser
His190 His190(44)A The residue acts as a proton acceptor from the nucleophilic Ser164 and as a proton donor to the departing methanol. Hydrogen bonding interactions with Asp 286 orientates the residue for interaction with Ser164, and also modifies the pKa of the general acid imidazole nitrogen towards proton donation. hydrogen bond donor, proton acceptor, proton donor, activator, electrostatic stabiliser
Ser164 Ser164(18)A The residue acts as a nucleophile towards the carbonyl functionality of the carboxyl-methylglutamate residues of the receptor substrate, resulting in an anionic tetrahedral intermediate. The hydroxyl proton of the residue is relayed to His 190, and then to the methanol leaving group. covalently attached, hydrogen bond donor, nucleophile, nucleofuge, proton donor, proton acceptor, activator
Met283 (main-N), Thr165 (main-N) Met283(137)A (main-N), Thr165(19)A (main-N) The residue's backbone forms an oxyanion hole which stabilises the anionic tetrahedral intermediate. hydrogen bond donor, electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic addition, proton transfer, overall reactant used, intermediate formation, enzyme-substrate complex formation, inferred reaction step, elimination (not covered by the Ingold mechanisms), intermediate collapse, overall product formed

References

  1. West AH et al. (1995), J Mol Biol, 250, 276-290. Crystal Structure of the Catalytic Domain of the Chemotaxis Receptor Methylesterase, CheB. DOI:10.1006/jmbi.1995.0376. PMID:7608974.
  2. Jurica MS et al. (1998), Structure, 6, 809-813. Mind your B's and R's: bacterial chemotaxis, signal transduction and protein recognition. DOI:10.1016/s0969-2126(98)00082-3.
  3. Djordjevic S et al. (1997), Structure, 5, 545-558. Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine. DOI:10.1016/s0969-2126(97)00210-4.

Catalytic Residues Roles

Residue Roles
Ser164(18)A activator, hydrogen bond donor
His190(44)A activator, hydrogen bond donor, electrostatic stabiliser
Asp286(140)A electrostatic stabiliser, hydrogen bond acceptor
Met283(137)A (main-N) hydrogen bond donor, electrostatic stabiliser
Thr165(19)A (main-N) hydrogen bond donor, electrostatic stabiliser
Ser164(18)A nucleophile
His190(44)A proton acceptor
Ser164(18)A proton donor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, overall reactant used, intermediate formation, enzyme-substrate complex formation, inferred reaction step

Catalytic Residues Roles

Residue Roles
Ser164(18)A activator, covalently attached, hydrogen bond donor
His190(44)A activator, hydrogen bond donor, electrostatic stabiliser
Asp286(140)A electrostatic stabiliser, hydrogen bond acceptor
Met283(137)A (main-N) hydrogen bond donor, electrostatic stabiliser
Thr165(19)A (main-N) hydrogen bond donor, electrostatic stabiliser
His190(44)A proton donor

Chemical Components

elimination (not covered by the Ingold mechanisms), proton transfer, intermediate formation, intermediate collapse, overall product formed

Catalytic Residues Roles

Residue Roles
Ser164(18)A activator, covalently attached
His190(44)A activator, hydrogen bond donor, electrostatic stabiliser
Asp286(140)A electrostatic stabiliser, hydrogen bond acceptor
Met283(137)A (main-N) hydrogen bond donor, electrostatic stabiliser
Thr165(19)A (main-N) hydrogen bond donor, electrostatic stabiliser
His190(44)A proton acceptor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, intermediate formation, overall reactant used

Catalytic Residues Roles

Residue Roles
Ser164(18)A activator, covalently attached
His190(44)A activator, hydrogen bond donor, electrostatic stabiliser
Asp286(140)A electrostatic stabiliser, hydrogen bond acceptor
Met283(137)A (main-N) hydrogen bond donor, electrostatic stabiliser
Thr165(19)A (main-N) hydrogen bond donor
Ser164(18)A nucleofuge, proton acceptor
His190(44)A proton donor

Chemical Components

elimination (not covered by the Ingold mechanisms), proton transfer, intermediate collapse, overall product formed

Contributors

Sophie T. Williams, Nozomi Nagano, Craig Porter, Gemma L. Holliday, James Willey