[ { "id": "authors:5j2x5-4c806", "collection": "authors", "collection_id": "5j2x5-4c806", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:QUEjbc05", "type": "article", "title": "Structural and chemical requirements for histidine phosphorylation by the chemotaxis kinase CheA", "author": [ { "family_name": "Quezada", "given_name": "Cindy M.", "clpid": "Quezada-C-M" }, { "family_name": "Hamel", "given_name": "Damon J.", "clpid": "Hamel-D-J" }, { "family_name": "Gradinaru", "given_name": "Cristian", "clpid": "Gradinaru-C" }, { "family_name": "Bilwes", "given_name": "Alexandrine M.", "clpid": "Bilwes-A-M" }, { "family_name": "Dahlquist", "given_name": "Frederick W.", "clpid": "Dahlquist-F-W" }, { "family_name": "Crane", "given_name": "Brian R.", "clpid": "Crane-B-R" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" } ], "abstract": "The CheA histidine kinase initiates the signal transduction pathway of bacterial chemotaxis by autophosphorylating a conserved histidine on its phosphotransferase domain (P1). Site-directed mutations of neighboring conserved P1 residues (Glu-67, Lys-48, and His-64) show that a hydrogen-bonding network controls the reactivity of the phospho-accepting His (His-45) in Thermotoga maritima CheA. In particular, the conservative mutation E67Q dramatically reduces phospho-transfer to P1 without significantly affecting the affinity of P1 for the CheA ATP-binding domain. High resolution crystallographic studies revealed that although all mutants disrupt the hydrogen-bonding network to varying degrees, none affect the conformation of His-45. N-15-NMR chemical shift studies instead showed that Glu-67 functions to stabilize the unfavored (NH)-H-delta 1 tautomer of His-45, thereby rendering the N-epsilon 2 imidazole unprotonated and well positioned for accepting the ATP phosphoryl group.", "doi": "10.1074/jbc.M505316200", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "2005-08-26", "series_number": "34", "volume": "280", "issue": "34", "pages": "30581-30585" }, { "id": "authors:qgn69-r1y68", "collection": "authors", "collection_id": "qgn69-r1y68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150407-123014690", "type": "article", "title": "The solution structure and interactions of CheW from Thermotoga maritima", "author": [ { "family_name": "Griswold", "given_name": "Ian J.", "clpid": "Griswold-I-J" }, { "family_name": "Zhou", "given_name": "Hongjun", "clpid": "Zhou-Hongjun" }, { "family_name": "Matison", "given_name": "Mikenzie", "clpid": "Matison-M" }, { "family_name": "Swanson", "given_name": "Ronald V.", "clpid": "Swanson-R-V" }, { "family_name": "McIntosh", "given_name": "Lawrence P.", "clpid": "McIntosh-L-P" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" }, { "family_name": "Dahlquist", "given_name": "Frederick W.", "clpid": "Dahlquist-F-W" } ], "abstract": "Using protein from the hyperthermophile Thermotoga maritima, we have determined the solution structure of CheW, an essential component in the formation of the bacterial chemotaxis signaling complex. The overall fold is similar to the regulatory domain of the chemotaxis kinase CheA. In addition, interactions of CheW with CheA were monitored by nuclear magnetic resonance (NMR) techniques. The chemical shift perturbation data show the probable contacts that CheW makes with CheA. In combination with previous genetic data, the structure also suggests a possible binding site for the chemotaxis receptor. These results provide a structural basis for a model in which CheW acts as a molecular bridge between CheA and the cytoplasmic tails of the receptor.", "doi": "10.1038/nsb753", "issn": "1072-8368", "publisher": "Nature Publishing Group", "publication": "Nature Structural Biology", "publication_date": "2002-02", "series_number": "2", "volume": "9", "issue": "2", "pages": "121-125" }, { "id": "authors:yymj0-sef41", "collection": "authors", "collection_id": "yymj0-sef41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170409-082224546", "type": "article", "title": "Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability", "author": [ { "family_name": "Usher", "given_name": "Ken C.", "clpid": "Usher-K-C" }, { "family_name": "de la Cruz", "given_name": "A. F.", "clpid": "de-la-Cruz-A-F" }, { "family_name": "Dahlquist", "given_name": "Frederick W.", "clpid": "Dahlquist-F-W" }, { "family_name": "Swanson", "given_name": "Ronald V.", "clpid": "Swanson-R-V" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" }, { "family_name": "Remington", "given_name": "S. James", "clpid": "Remington-S-J" } ], "abstract": "The crystal structure of CheY protein from Thermotoga maritima has been determined in four crystal forms with and without Mg++ bound, at up to 1.9 A resolution. Structural comparisons with CheY from Escherichia coli shows substantial similarity in their folds, with some concerted changes propagating away from the active site that suggest how phosphorylated CheY, a signal transduction protein in bacterial chemotaxis, is recognized by its targets. A highly conserved segment of the protein (the \"y-turn loop,\" residues 55-61), previously suggested to be a rigid recognition determinant, is for the first time seen in two alternative conformations in the different crystal structures. Although CheY from Thermotoga has much higher thermal stability than its mesophilic counterparts, comparison of structural features previously proposed to enhance thermostability such as hydrogen bonds, ion pairs, compactness, and hydrophobic surface burial would not suggest it to be so.", "doi": "10.1002/pro.5560070221", "pmcid": "PMC2143910", "issn": "0961-8368", "publisher": "Wiley", "publication": "Protein Science", "publication_date": "1998-02", "series_number": "2", "volume": "7", "issue": "2", "pages": "403-412" }, { "id": "authors:ksd52-9m982", "collection": "authors", "collection_id": "ksd52-9m982", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171129-105830297", "type": "article", "title": "Phosphotransfer and CheY-Binding Domains of the Histidine Autokinase CheA Are Joined by a Flexible Linker", "author": [ { "family_name": "Zhou", "given_name": "Hongjun", "clpid": "Zhou-Hongjun" }, { "family_name": "McEvoy", "given_name": "Megan M.", "clpid": "McEvoy-M-M" }, { "family_name": "Lowry", "given_name": "David F.", "clpid": "Lowry-D-F" }, { "family_name": "Swanson", "given_name": "Ronald V.", "clpid": "Swanson-R-V" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" }, { "family_name": "Dahlquist", "given_name": "Frederick W.", "clpid": "Dahlquist-F-W" } ], "abstract": "Multidimensional heteronuclear NMR techniques were applied to study a protein fragment of the histidine autokinase CheA from Escherichia coli. This fragment (CheA_(1-233)) contains the phosphotransfer domain and the CheY-binding domain joined by a linker region. Comparison of chemical shift and NOE cross-peak patterns indicates that the structures of the two domains in CheA_(1-233) remain nearly the same as in the two individual domain fragments, CheA1-134 and CheA_(124-257). Relaxation properties of the backbone ^(15)N nuclei were measured to study the rotational correlations of the two domains and properties of the linker region. Dynamics data were analyzed both by an isotropic motional model and an anisotropic motional model. The experimental T_1 and T_2 values, the derived rotational correlation times, and motional anisotropy are significantly different for the two domains, indicating the two domains reorient independently and the linker region is highly flexible. Dynamics data of CheA_(1-233) were also compared with those of CheA_(1-134). Our studies show that flexible domain linkers and extended and flexible terminal polypeptide chains can have significant effects on the motional properties of the adjacent structured regions. These observations suggest a model for the graded regulation of CheA autophosphorylation activity. In this model, the various activity states of the receptor are generated by controlling the access of the mean position of the kinase domain to the phosphotransfer domain. This would then modulate the diffusional encounter rate of the domains and hence activity over a wide and graded range of values.", "doi": "10.1021/bi951960e", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1996-01-16", "series_number": "2", "volume": "35", "issue": "2", "pages": "433-443" }, { "id": "authors:ywcby-xnd41", "collection": "authors", "collection_id": "ywcby-xnd41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180206-065820046", "type": "article", "title": "NMR studies of the phosphotransfer domain of the histidine kinase CheA from Escherichia coli: assignments, secondary structure, general fold, and backbone dynamics", "author": [ { "family_name": "Zhou", "given_name": "Hongjun", "clpid": "Zhou-Hongjun" }, { "family_name": "Lowry", "given_name": "David F.", "clpid": "Lowry-D-F" }, { "family_name": "Swanson", "given_name": "Ronald V.", "clpid": "Swanson-R-V" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" }, { "family_name": "Dahlquist", "given_name": "Frederick W.", "clpid": "Dahlquist-F-W" } ], "abstract": "Multidimensional heteronuclear NMR techniques were applied to study the phosphotransfer domain, residues 1 - 134, of the histidine kinase CheA, from Escherichia coli, which contains the site of autophosphorylation, His48. Assignments of the backbone amide groups and side chain patons are nearly complete. Our studies show that this protein fragment consists of five a-helices (A-E)connected by turns. Analysis of NOE distance restraints provided by two-dimensional (2D) ^1H-^1H and three-dimensional (3D) ^(15)N-edited NOESY spectra using model building and structure calculations indicates that the five helices form an antiparallel helix bundle with near-neighbor connectivity. The amino-tenninal four helices are proposed to be arranged in a right-handed manner with helix E packing against helices C and D. From ideal hydrophobic helical packing and structure calculations, the site of autophosphorylation, His48, is nearly fully exposed to the solvent. We measured the NMR relaxation properties of the backbone ^(15)N nuclei using inverse detected two-dimensional NMR spectroscopy. The protein backbone dynamics studies show that CheA1-134 is formed into a tight and compact structure with very limited flexibilities both in\nhelices and turns. Structural implications of titration and phosphorylation experiments are briefly discussed.", "doi": "10.1021/bi00042a018", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "1995-10-24", "series_number": "42", "volume": "34", "issue": "42", "pages": "13858-13870" }, { "id": "authors:e2cr4-y0y21", "collection": "authors", "collection_id": "e2cr4-y0y21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150624-142751543", "type": "article", "title": "Localized perturbations in CheY structure monitored by NMR identify a CheA binding interface", "author": [ { "family_name": "Swanson", "given_name": "Ronald V.", "clpid": "Swanson-R-V" }, { "family_name": "Lowry", "given_name": "David F.", "clpid": "Lowry-D-F" }, { "family_name": "Matsumura", "given_name": "Philip", "clpid": "Matsumura-P" }, { "family_name": "McEvoy", "given_name": "Megan M.", "clpid": "McEvoy-M-M" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" }, { "family_name": "Dahlquist", "given_name": "Frederick W.", "clpid": "Dahlquist-F-W" } ], "abstract": "Phosphotransfer between the autophosphorylating histidine kinase CheA and the response regulator CheY represents a crucial step in the bacterial chemotaxis signal transduction pathway. The ^(15)N\u2212^1H correlation spectrum of CheY complexed with an amino-terminal fragment of CheA exhibits specific localized differences in chemical shifts when compared to the spectrum of uncompiexed CheY. When mapped onto the three-dimensional structure of CheY, these changes define a region distinct from the active site. A single amino-acid substitution within this binding region on CheY, alanine to valine at position 103, significantly decreases the affinity of CheY for CheA. The binding face described by these changes partially overlaps a flagellar switch binding surface previously defined by mutagenesis.", "doi": "10.1038/nsb1095-906", "issn": "1072-8368", "publisher": "Nature Publishing Group", "publication": "Nature Structural Biology", "publication_date": "1995-10", "series_number": "10", "volume": "2", "issue": "10", "pages": "906-910" }, { "id": "authors:5rf0s-hjv02", "collection": "authors", "collection_id": "5rf0s-hjv02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KEHpnas83", "type": "article", "title": "Enzymatic deamidation of methyl-accepting chemotaxis proteins in Escherichia coli catalyzed by the cheB gene product", "author": [ { "family_name": "Kehry", "given_name": "Marilyn R.", "clpid": "Kehry-M-R" }, { "family_name": "Bond", "given_name": "Martha W.", "clpid": "Bond-M-W" }, { "family_name": "Hunkapiller", "given_name": "Michael W.", "clpid": "Hunkapiller-M-W" }, { "family_name": "Dahlquist", "given_name": "Frederick W.", "clpid": "Dahlquist-F-W" } ], "abstract": "The methyl-accepting chemotaxis proteins (MCPs) of Escherichia coli undergo reversible methylation that has been correlated with adaptation of cells to environmental stimuli. MCPI, the product of the tsr gene, accepts methyl groups at multiple sites that are located on two tryptic peptides, denoted K1 and R1. A second modification of the MCPs, which is not methylation, has been designated the CheB-dependent modification. A CheB-dependent modification occurs on methyl-accepting peptide K1 and allows additional methyl groups to be incorporated into this peptide. We have performed partial amino acid sequence analyses on radiolabeled peptides K1 and R1 derived from MCPI and have identified several methyl-accepting sites. We found that, in the absence of CheB-dependent modification, a site in peptide K1 is unable to accept methyl groups. Correlation of this protein sequence data with the nucleotide sequence of the tsr gene [Boyd, A., Kendall, K. & Simon, M. I. (1983) Nature (London) 301, 623-626] suggests that CheB-dependent modification of MCPI is the enzymatic deamidation of glutamine to methyl-accepting glutamic acid. Possible roles for this deamidation in bacterial chemotaxis are discussed.", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1983-06-15", "series_number": "12", "volume": "80", "issue": "12", "pages": "3599-3603" }, { "id": "authors:whzg6-ymg08", "collection": "authors", "collection_id": "whzg6-ymg08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:RAFpnas69", "type": "article", "title": "The use of nuclear magnetic resonance to describe relative modes of binding to lysozyme of homologous inhibitors and related substrates", "author": [ { "family_name": "Raftery", "given_name": "M. A.", "clpid": "Raftery-M-A" }, { "family_name": "Dahlquist", "given_name": "F. W.", "clpid": "Dahlquist-F-W" }, { "family_name": "Parsons", "given_name": "S. M.", "clpid": "Parsons-S-M" }, { "family_name": "Wolcott", "given_name": "R. G.", "clpid": "Wolcott-R-G" } ], "abstract": "Proton magnetic resonance has been used to study the association of inhibitors and substrates with hen egg-white lysozyme. Changes in chemical shift, due to association, of acetamido methyl group resonances of the small molecules have been quantitated. This has allowed definition of magnetic parameters for three contiguous binding subsites on the enzyme surface. The relative modes of occupancy of these sites by N-acetyl-D-glucosamine (NAG), chitobiose, chitotriose, their methyl glycosides, and chitotetraose have been delineated. In addition, the binding to these sites of N-acetyl-D-muramic acid (NAM) and a cell-wall disaccharide, NAG-NAM, have been studied. There is good, although not complete, agreement between the results obtained and X-ray analysis studies of the binding of some of these inhibitors to crystalline lysozyme. Binding of synthetic substrates, such as p-nitrophenyl-2-acetamido-4-O-(2-acetamido-2-deoxy-\u00df -D-glucopyranosyl)-\u00df -D-glucopyranoside (NAG-Gluc- \u03a6NO2), has also been studied by the magnetic resonance technique described.", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1969-01-01", "series_number": "1", "volume": "62", "issue": "1", "pages": "44-51" }, { "id": "authors:kgc25-mwp49", "collection": "authors", "collection_id": "kgc25-mwp49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:DAHpnas68", "type": "article", "title": "Demonstration of carbonium ion intermediate during lysozyme catalysis", "author": [ { "family_name": "Dahlquist", "given_name": "F. W.", "clpid": "Dahlquist-F-W" }, { "family_name": "Rand-Meir", "given_name": "T.", "clpid": "Rand-Meir-T" }, { "family_name": "Raftery", "given_name": "M. A.", "clpid": "Raftery-M-A" } ], "abstract": "X-ray analysis studies (1,2) on the relative modes of association of various inhibitors and substrates with lysozyme have led to a proposal for the catalytic mechanism of the enzyme (3,4). This proposal suggests that the enzyme catalyzes the formation of a carbonium ion at C1 of the glycosidic bond undergoing hydrolysis and, further, provides it with steric and electrostatic stabilization. To date, little evidence of a chemical nature has been available to test the mechanistic proposal.", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1968-12-01", "series_number": "4", "volume": "61", "issue": "4", "pages": "1194-1198" }, { "id": "authors:demyy-dq489", "collection": "authors", "collection_id": "demyy-dq489", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:RAFjbc68", "type": "article", "title": "A Proton Magnetic Resonance Study of the Association of Lysozyme with Monosaccharide Inhibitors", "author": [ { "family_name": "Raftery", "given_name": "M. A.", "clpid": "Raftery-M-A" }, { "family_name": "Dahlquist", "given_name": "F. W.", "clpid": "Dahlquist-F-W" }, { "family_name": "Chan", "given_name": "S. I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Parsons", "given_name": "S. M.", "clpid": "Parsons-S-M" } ], "abstract": "It has been shown that the acetamido methyl protons of N-acetyl-d-glucosamine undergo a chemical shift to higher fields in their proton magnetic resonance spectrum when the inhibitor is bound to lysozyme. The observed chemical shift in the presence of the enzyme is different for the agr- and \u00df-anomeric forms of 2-acetamido-2-deoxy-d-glucopyranose indicating either a difference in the affinity of the anomeric forms for lysozyme or different magnetic environments for the methyl protons in their enzyme-bound state. That the agr- and \u00df-anomeric forms of GlcAc bind to lysozyme in a competitive fashion was indicated by observing the proton magnetic resonance spectra in the presence of 2-acetamido-d3-2-deoxy-agr-d-glucopyranose. The methyl glycosides, methyl-agr-GlcAc and methyl-\u00df-GlcAc, were also shown to bind competitively with both anomers of GlcAc. Quantitative analysis of the chemical shift data observed for the association of GlcAc with lysozyme was complicated by the mutarotation of GlcAc between its agr- and \u00df-anomeric forms. However, in the case of the methyl glucosides, where the conformation of each anomer is frozen, it was possible to analyze the chemical shift data in a straightforward manner, and the dissociation constant as well as the chemical shift of the acetamido methyl protons of the enzyme-inhibitor complex was determined for both anomers. The results indicate that the two anomers of methyl-GlcAc bind to lysozyme with slightly different affinities but that the acetamido methyl groups of both anomers experience identical magnetic environments in the enzyme-inhibitor complex.", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "1968-08-25", "series_number": "16", "volume": "243", "issue": "16", "pages": "4175-4180" } ]