Abstract:
:The crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-A resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5' hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5'-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme.
journal_name
J Bacterioljournal_title
Journal of bacteriologyauthors
Safo MK,Musayev FN,Hunt S,di Salvo ML,Scarsdale N,Schirch Vdoi
10.1128/JB.186.23.8074-8082.2004keywords:
subject
Has Abstractpub_date
2004-12-01 00:00:00pages
8074-82issue
23eissn
0021-9193issn
1098-5530pii
186/23/8074journal_volume
186pub_type
杂志文章abstract::Three independently isolated metK mutants have been shown to have leisions lying between speB and glc near 57 min on the Escherichia coli chromosome. Two deletions result in a lack of the metC gene product but neither extends into the metK glc region. The three metK mutations are recessive to the wild-type allele carr...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.122.3.1144-1152.1975
更新日期:1975-06-01 00:00:00
abstract::Purified suspensions of Chlamydia psittaci were prepared from L cells. Thin sections of intact elementary bodies and intact developmental reticulate bodies and of their purified envelopes were observed by electron microscopy. In both intact organisms and partially purified envelopes, two membranous structures, each ap...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.105.1.355-360.1971
更新日期:1971-01-01 00:00:00
abstract::The DNA region encoding early nodulation functions of Bradyrhizobium japonicum 3I1b110 (I110) was isolated by its homology to the functionally similar region from Rhizobium meliloti. Isolation of a number of overlapping recombinant clones from this region allowed the construction of a restriction map of the region. Th...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.164.3.1301-1308.1985
更新日期:1985-12-01 00:00:00
abstract::The potent tumor-promoting agent croton oil, which has been shown previously to be strongly mitogenic in mammalian cells, stimulates cell division in snake mutants of the blue-green bacterium Agmenellum quadruplicatum. ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.114.2.874-875.1973
更新日期:1973-05-01 00:00:00
abstract::Germination of dormant Bacillus subtilis spores with specific nutrient germinants is dependent on a number of inner membrane (IM) proteins, including (i) the GerA, GerB, and GerK germinant receptors (GRs) that respond to nutrient germinants; (ii) the GerD protein, essential for optimal GR function; and (iii) SpoVA pro...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.00377-13
更新日期:2013-08-01 00:00:00
abstract::Production of deoxyribonucleotides for DNA synthesis is an essential and tightly regulated process. The class Ia ribonucleotide reductase (RNR), the product of the nrdAB genes, is required for aerobic growth of Escherichia coli. In catalyzing the reduction of ribonucleotides, two of the cysteines of RNR become oxidize...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.05989-11
更新日期:2012-03-01 00:00:00
abstract::Evidence of the presence of messenger ribonucleic acid (mRNA) in dormant spores of Bacillus subtilis has been obtained. The bulk RNA from spores was isolated and labeled in vitro with tritiated dimethyl sulfate. The spore RNA hybridized to 2.4 to 3.2% of the B. subtilis genome. The RNA hybridized to both the complemen...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.119.2.514-521.1974
更新日期:1974-08-01 00:00:00
abstract::A group of proteic toxin-antitoxin (TA) cassettes whose representatives are widely distributed among bacterial genomes has been identified. These cassettes occur in chromosomes, plasmids, bacteriophages, and noncomposite transposons, as well as in the SXT conjugative element of Vibrio cholerae. The following four homo...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01610-06
更新日期:2007-03-01 00:00:00
abstract::A draft genome sequence of Tsukamurella sp., an aerobic bacterium isolated from a human sputum specimen, is described here. A new virus or provirus, TPA4, was characterized. ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01279-12
更新日期:2012-10-01 00:00:00
abstract::Pasteurella multocida is the causative agent of a range of diseases with economic importance in production animals. Many systems have been employed to identify virulence factors of P. multocida, including in vivo expression technology (IVET), signature-tagged mutagenesis, and whole-genome expression profiling. In a pr...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.187.7.2278-2285.2005
更新日期:2005-04-01 00:00:00
abstract::Impurities believed to be polysaccharides have been found in mycobacterial deoxyribonucleic acid (DNA) preparations. Agar-gel diffusion of the DNA preparations against concanavalin A indicated the presence of three polysaccharides and was used to follow the purification procedures. The polysaccharides appeared to be t...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.112.3.1033-1039.1972
更新日期:1972-12-01 00:00:00
abstract::2-Carboxybenzaldehyde dehydrogenase from the phenanthrene-degrading bacterium Nocardioides sp. strain KP7 was purified and characterized. The purified enzyme had a molecular mass of 53 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 205 kDa by gel filtration chromatography. Thus, the homotetramer ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.179.20.6488-6494.1997
更新日期:1997-10-01 00:00:00
abstract::Nishida, S. (Kanazawa University, Kanazawa, Japan), and G. Nakagawara. Isolation of toxigenic strains of Clostridium novyi from soil. J. Bacteriol. 88:1636-1640. 1964.-The cultural conditions for toxin production by Clostridium novyi were investigated, and the optimal constituents of a proper medium were determined. A...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.88.6.1636-1640.1964
更新日期:1964-12-01 00:00:00
abstract::Bacteroides thetaiotaomicron, a gram-negative obligate anaerobe, appears to utilize starch by first binding the polymer to its surface and then translocating it into the periplasmic space. Several genes that encode enzymes or outer membrane proteins involved in starch utilization have been identified. These have been ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.178.24.7180-7186.1996
更新日期:1996-12-01 00:00:00
abstract::Commonly used procedures effected the extraction of only 10% of the lipoteichoic acid of stationary-phase cells of Staphylococcus aureus and Streptococcus faecium, unless the cells were first disrupted. ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.149.1.399-402.1982
更新日期:1982-01-01 00:00:00
abstract::A strain of Serratia marcescens was found to produce a bacteriocin that inhibits the growth of certain Escherichia coli strains. This inhibition was bacteriocidal rather than bacteriostatic and was not caused by a bacteriophage. Whereas the bacteriocin was inactive on the 7 Serratia strains tested, it killed 11 of the...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.99.3.655-660.1969
更新日期:1969-09-01 00:00:00
abstract::Helicobacter pylori strains can be divided into two groups, based on the presence of two unrelated genes, iceA1 and iceA2, that occupy the same genomic locus. hpyIM, located immediately downstream of either gene, encodes a functional CATG-specific methyltransferase. Despite the strong conservation of the hpyIM open re...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.183.13.3875-3884.2001
更新日期:2001-07-01 00:00:00
abstract::Hottle, G. A. (Naval Biological Laboratory, University of California, Berkeley), and D. N. Wright. Growth and survival of Mycoplasma neurolyticum in liquid media. J. Bacteriol. 91:1834-1839. 1966.-Maximal growth of Mycoplasma neurolyticum (between 10(8) and 10(9) colony-forming units per ml) was obtained after 3 days ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.91.5.1834-1839.1966
更新日期:1966-05-01 00:00:00
abstract::The genetic transformation mutant Rd(DB117)rec- has a pleiotropic phenotype that includes reduced levels of phage recombination. Physical mapping experiments showed that this strain has a 78.5-kbp insertion in the rec-2 gene. The rec-2 dependence of phage recombination was reexamined to determine whether the defective...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.174.15.4960-4966.1992
更新日期:1992-08-01 00:00:00
abstract::Nine high copy number mutations of plasmid R6-5, representing five phenotypically distinct groups, have been identified by DNA sequencing. In each mutant plasmid examined, a single nucleotide change was found. The effects of the mutations on possible gene products, and DNA-RNA secondary structure, were analyzed and co...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.154.1.429-436.1983
更新日期:1983-04-01 00:00:00
abstract::Some bacteriophages target potentially pathogenic bacteria by exploiting surface-associated virulence factors as receptors. For example, phage have been identified that exhibit specificity for Vi capsule producing Salmonella enterica serovar Typhi. Here we have characterized the Vi-associated E1-typing bacteriophage u...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01654-07
更新日期:2008-04-01 00:00:00
abstract::The genes that encode the two subunits of Bacillus subtilis phenylalanyl-tRNA synthetase were cloned from alpha lambda library of chromosomal B. subtilis DNA by specific complementation of a thermosensitive Escherichia coli pheS mutation. Both genes (we named them pheS and pheT, analogous to the corresponding genes of...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.171.2.1228-1232.1989
更新日期:1989-02-01 00:00:00
abstract::A method was devised for the isolation of yeast monomorphic (LEV) mutants of Candida albicans. By this procedure, about 20 stable yeast-like mutants were isolated after mutagenesis with ethyl methane sulfonate. The growth rate of the mutants in different carbon sources, both fermentable and not, was indistinguishable ...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.176.8.2318-2325.1994
更新日期:1994-04-01 00:00:00
abstract::Rogosa, M. (National Institutes of Health, Bethesda, Md.). The genus Veillonella. I. General cultural, ecological, and biochemical considerations. J. Bacteriol. 87:162-170. 1964.-Arguments are presented for excluding Veillonella discoides, V. reniformis, V. orbiculus, and V. vulvovaginitidis from the genus, and for re...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.87.1.162-170.1964
更新日期:1964-01-01 00:00:00
abstract::The replication of the R factor Rts1 in Proteus mirabilis was examined by using the technique of CsCl density-gradient centrifugation. The proportion of Rts1 deoxyribonucleic acid (DNA) relative to the host chromosomal DNA (% R-DNA) was 7% in both exponential and stationary growth phases in Penassay Broth and suppleme...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.109.2.492-498.1972
更新日期:1972-02-01 00:00:00
abstract::The Bacillus subtilis enzymes ExoA and Nfo (originally termed YqfS) are endonucleases that can repair apurinic/apyrimidinic (AP) sites and strand breaks in DNA. We have analyzed how the lack of ExoA and Nfo affects the resistance of growing cells and dormant spores of B. subtilis to a variety of treatments, some of wh...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.187.21.7374-7381.2005
更新日期:2005-11-01 00:00:00
abstract::The sheath of the filamentous, gliding cyanobacterium Phormidium uncinatum was studied by using light and electron microscopy. In thin sections and freeze fractures the sheath was found to be composed of helically arranged carbohydrate fibrils, 4 to 7 nm in diameter, which showed a substantial degree of crystallinity....
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.180.15.3923-3932.1998
更新日期:1998-08-01 00:00:00
abstract::To isolate strains with new recA mutations that differentially affect RecA protein functions, we mutagenized in vitro the recA gene carried by plasmid mini-F and then introduced the mini-F-recA plasmid into a delta recA host that was lysogenic for prophage phi 80 and carried a lac duplication. By scoring prophage indu...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/jb.171.5.2415-2423.1989
更新日期:1989-05-01 00:00:00
abstract::The products of phospholipid turnover in Bacillus stearothermophilus were determined in cultures labeled to equilibrium and with short pulses of [32P]phosphate and [2-3H]glycerol. Label lost from the cellular lipid pool was recovered in three fractions: low-molecular-weight extracellular products, extracellular lipid,...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.154.1.294-303.1983
更新日期:1983-04-01 00:00:00
abstract::The rice pathogen recognition receptor, XA21, confers resistance to Xanthomonas oryzae pv. oryzae strains producing the type one system-secreted molecule, AvrXA21. X. oryzae pv. oryzae requires a regulatory two-component system (TCS) called RaxRH to regulate expression of eight rax (required for AvrXA21 activity) gene...
journal_title:Journal of bacteriology
pub_type: 杂志文章
doi:10.1128/JB.01406-07
更新日期:2008-03-01 00:00:00