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PDBsum entry 1chd

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Carboxyl methylesterase PDB id
1chd
Jmol
Contents
Protein chain
198 a.a. *
Waters ×123
* Residue conservation analysis
PDB id:
1chd
Name: Carboxyl methylesterase
Title: Cheb methylesterase domain
Structure: Cheb methylesterase. Chain: a. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 99287. Strain: lt2. Gene: cheb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.75Å     R-factor:   0.182     R-free:   0.230
Authors: A.H.West,E.Martinez-Hackert,A.M.Stock
Key ref:
A.H.West et al. (1995). Crystal structure of the catalytic domain of the chemotaxis receptor methylesterase, CheB. J Mol Biol, 250, 276-290. PubMed id: 7608974 DOI: 10.1006/jmbi.1995.0376
Date:
09-Mar-95     Release date:   29-Jan-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04042  (CHEB_SALTY) -  Chemotaxis response regulator protein-glutamate methylesterase
Seq:
Struc:
349 a.a.
198 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.61  - Protein-glutamate methylesterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein L-glutamate O5-methyl ester + H2O = protein L-glutamate + methanol
Protein L-glutamate O(5)-methyl ester
+ H(2)O
= protein L-glutamate
+ methanol
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     chemotaxis   2 terms 
  Biochemical function     two-component response regulator activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1995.0376 J Mol Biol 250:276-290 (1995)
PubMed id: 7608974  
 
 
Crystal structure of the catalytic domain of the chemotaxis receptor methylesterase, CheB.
A.H.West, E.Martinez-Hackert, A.M.Stock.
 
  ABSTRACT  
 
Signaling activity of bacterial chemotaxis transmembrane receptors is modulated by reversible covalent modification of specific receptor glutamate residues. The level of receptor methylation results from the activities of a specific S-adenosylmethionine-dependent methyltransferase, CheR, and the CheB methylesterase, which catalyzes hydrolysis of receptor glutamine or methylglutamate side-chains to glutamic acid. The CheB methylesterase belongs to a large family of response regulator proteins in which N-terminal regulatory domains control the activities of C-terminal effector domains. The crystal structure of the catalytic domain of the Salmonella typhimurium CheB methylesterase has been determined at 1.75 A resolution. The domain has a modified, doubly wound alpha/beta fold in which one of the helices is replaced by an anti-parallel beta-hairpin. Previous biochemical and mutagenesis data, suggest that the methylester hydrolysis catalyzed by CheB proceeds through a mechanism involving a serine nucleophile. The methylesterase active site is tentatively identified as a cleft at the C-terminal edge of the beta-sheet containing residues Ser164, His190 and Asp286. The three-dimensional fold, and the arrangement of residues within the catalytic triad distinguishes the CheB methylesterase from any previously described serine protease or serine hydrolase.
 
  Selected figure(s)  
 
Figure 8.
Figure 8. Stereo view of the proposed active site region of the CheBmethylesterase displaying the catalytic triad residues, Ser164, His190 and Asp286. Residues Asn254, Ser259, Val260 and Asp261, located in the loop that connects strand b6 to helix aC, form hydrogen bonds with the carboxylate oxygen atoms of Asp286. The image was displayed using the program O (Jones et al., 1991).
Figure 10.
Figure 10. Comparison of the catalytic triads of a serine protease, the CheB methylesterase, and a thiol protease. Stereo views of the catalytic triads of (a) subtilisin BPN' (Pantoliano et al., 1989), (b) CheB and (c) papain (Drenth et al., 1971), are shown with the imidazole rings of the histidine residues aligned in similar orientations. The nucleophile in CheB and in papain is on the opposite side of the imidazole ring relative to the nucleophile in subtilisin. Images were drawn with MOLSCRIPT (Kraulis, 1991).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 250, 276-290) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21292743 D.Kanungpean, T.Kakuda, and S.Takai (2011).
Participation of CheR and CheB in the chemosensory response of Campylobacter jejuni.
  Microbiology, 157, 1279-1289.  
20226724 M.Y.Galperin (2010).
Diversity of structure and function of response regulator output domains.
  Curr Opin Microbiol, 13, 150-159.  
19747079 Z.Li, and J.B.Stock (2009).
Protein carboxyl methylation and the biochemistry of memory.
  Biol Chem, 390, 1087-1096.  
17339222 E.Bantinaki, R.Kassen, C.G.Knight, Z.Robinson, A.J.Spiers, and P.B.Rainey (2007).
Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity.
  Genetics, 176, 441-453.  
17908686 T.J.Muff, and G.W.Ordal (2007).
The CheC phosphatase regulates chemotactic adaptation through CheD.
  J Biol Chem, 282, 34120-34128.  
16369945 M.D.Baker, P.M.Wolanin, and J.B.Stock (2006).
Signal transduction in bacterial chemotaxis.
  Bioessays, 28, 9.  
  16877318 M.K.Ashby (2006).
Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota.
  Archaea, 2, 11-30.  
16469702 X.Chao, T.J.Muff, S.Y.Park, S.Zhang, A.M.Pollard, G.W.Ordal, A.M.Bilwes, and B.R.Crane (2006).
A receptor-modifying deamidase in complex with a signaling phosphatase reveals reciprocal regulation.
  Cell, 124, 561-571.
PDB code: 2f9z
15653746 W.Zhang, J.S.Olson, and G.N.Phillips (2005).
Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis.
  Biophys J, 88, 2801-2814.  
14555659 Y.Kim, A.F.Yakunin, E.Kuznetsova, X.Xu, M.Pennycooke, J.Gu, F.Cheung, M.Proudfoot, C.H.Arrowsmith, A.Joachimiak, A.M.Edwards, and D.Christendat (2004).
Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum.
  J Biol Chem, 279, 517-526.
PDB code: 1l6r
12962628 W.Zhang, and G.N.Phillips (2003).
Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry.
  Structure, 11, 1097-1110.
PDB codes: 1or4 1or6
11912013 J.Marchant, B.Wren, and J.Ketley (2002).
Exploiting genome sequence: predictions for mechanisms of Campylobacter chemotaxis.
  Trends Microbiol, 10, 155-159.  
12119291 M.N.Levit, and J.B.Stock (2002).
Receptor methylation controls the magnitude of stimulus-response coupling in bacterial chemotaxis.
  J Biol Chem, 277, 36760-36765.  
10318862 E.Ogris, X.Du, K.C.Nelson, E.K.Mak, X.X.Yu, W.S.Lane, and D.C.Pallas (1999).
A protein phosphatase methylesterase (PME-1) is one of several novel proteins stably associating with two inactive mutants of protein phosphatase 2A.
  J Biol Chem, 274, 14382-14391.  
10350484 M.N.Levit, Y.Liu, and J.B.Stock (1999).
Mechanism of CheA protein kinase activation in receptor signaling complexes.
  Biochemistry, 38, 6651-6658.  
9687374 M.S.Jurica, and B.L.Stoddard (1998).
Mind your B's and R's: bacterial chemotaxis, signal transduction and protein recognition.
  Structure, 6, 809-813.  
9465023 S.Djordjevic, P.N.Goudreau, Q.Xu, A.M.Stock, and A.H.West (1998).
Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain.
  Proc Natl Acad Sci U S A, 95, 1381-1386.
PDB code: 1a2o
9016718 E.Martínez-Hackert, and A.M.Stock (1997).
The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor.
  Structure, 5, 109-124.
PDB code: 1opc
9442881 J.J.Falke, R.B.Bass, S.L.Butler, S.A.Chervitz, and M.A.Danielson (1997).
The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes.
  Annu Rev Cell Dev Biol, 13, 457-512.  
9434897 M.M.McEvoy, and F.W.Dahlquist (1997).
Phosphohistidines in bacterial signaling.
  Curr Opin Struct Biol, 7, 793-797.  
9115443 S.Djordjevic, and A.M.Stock (1997).
Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine.
  Structure, 5, 545-558.
PDB code: 1af7
9405352 Y.Liu, M.Levit, R.Lurz, M.G.Surette, and J.B.Stock (1997).
Receptor-mediated protein kinase activation and the mechanism of transmembrane signaling in bacterial chemotaxis.
  EMBO J, 16, 7231-7240.  
8650216 J.Lee, Y.Chen, T.Tolstykh, and J.Stock (1996).
A specific protein carboxyl methylesterase that demethylates phosphoprotein phosphatase 2A in bovine brain.
  Proc Natl Acad Sci U S A, 93, 6043-6047.  
8662838 M.J.Guimarães, J.F.Bazan, J.Castagnola, S.Diaz, N.G.Copeland, D.J.Gilbert, N.A.Jenkins, A.Varki, and A.Zlotnik (1996).
Molecular cloning and characterization of lysosomal sialic acid O-acetylesterase.
  J Biol Chem, 271, 13697-13705.  
8749361 A.M.Stock, and S.L.Mowbray (1995).
Bacterial chemotaxis: a field in motion.
  Curr Opin Struct Biol, 5, 744-751.  
  7556066 J.Rudolph, N.Tolliday, C.Schmitt, S.C.Schuster, and D.Oesterhelt (1995).
Phosphorylation in halobacterial signal transduction.
  EMBO J, 14, 4249-4257.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.