Structural characterization of a modification subunit of a putative type I restriction enzyme fromVibrio vulnificusYJ016

2012 ◽  
Vol 68 (11) ◽  
pp. 1570-1577 ◽  
Author(s):  
Suk-Youl Park ◽  
Hyun-Ju Lee ◽  
Jung-Mi Song ◽  
Jiali Sun ◽  
Hyo-Jeong Hwang ◽  
...  
Keyword(s):  
Vibrio Vulnificus ◽  
Restriction Enzymes ◽  
Type I ◽  
Aromatic Rings ◽  
Recognition Sequence ◽  
Thermus Aquaticus ◽  
Methyl Group ◽  
Cofactor Binding ◽  
Adenine Ring ◽  
Adenine Base

In multifunctional type I restriction enzymes, active methyltransferases (MTases) are constituted of methylation (HsdM) and specificity (HsdS) subunits. In this study, the crystal structure of a putative HsdM subunit fromVibrio vulnificusYJ016 (vvHsdM) was elucidated at a resolution of 1.80 Å. A cofactor-binding site forS-adenosyl-L-methionine (SAM, a methyl-group donor) is formed within the C-terminal domain of an α/β-fold, in which a number of residues are conserved, including the GxGG and (N/D)PP(F/Y) motifs, which are likely to interact with several functional moieties of the SAM methyl-group donor. Comparison with the N6 DNA MTase ofThermus aquaticusand other HsdM structures suggests that two aromatic rings (Phe199 and Phe312) in the motifs that are conserved among the HsdMs may sandwich both sides of the adenine ring of the recognition sequence so that a conserved Asn residue (Asn309) can interact with the N6 atom of the target adenine base (a methyl-group acceptor) and locate the target adenine base close to the transferred SAM methyl group.

scholarly journals Classical Xanthinuria in Nine Israeli Families and Two Isolated Cases from Germany: Molecular, Biochemical and Population Genetics Aspects

Biomedicines ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 788
Author(s):  
Hava Peretz ◽  
Ayala Lagziel ◽  
Florian Bittner ◽  
Mustafa Kabha ◽  
Meirav Shtauber-Naamati ◽  
...  
Keyword(s):  
Autosomal Recessive ◽  
Heterologous Protein ◽  
Heterologous Protein Expression ◽  
Type I ◽  
Type Ii ◽  
Amino Acid Residues ◽  
Cysteine Desulfurase ◽  
Cofactor Binding ◽  
Pathogenic Variants ◽  
Expression Studies

Classical xanthinuria is a rare autosomal recessive metabolic disorder caused by variants in the XDH (type I) or MOCOS (type II) genes. Thirteen Israeli kindred (five Jewish and eight Arab) and two isolated cases from Germany were studied between the years 1997 and 2013. Four and a branch of a fifth of these families were previously described. Here, we reported the demographic, clinical, molecular and biochemical characterizations of the remaining cases. Seven out of 20 affected individuals (35%) presented with xanthinuria-related symptoms of varied severity. Among the 10 distinct variants identified, six were novel: c.449G>T (p.(Cys150Phe)), c.1434G>A (p.(Trp478*)), c.1871C>G (p.(Ser624*)) and c.913del (p.(Leu305fs*1)) in the XDH gene and c.1046C>T (p.(Thr349Ileu)) and c.1771C>T (p.(Pro591Ser)) in the MOCOS gene. Heterologous protein expression studies revealed that the p.Cys150Phe variant within the Fe/S-I cluster-binding site impairs XDH biogenesis, the p.Thr349Ileu variant in the NifS-like domain of MOCOS affects protein stability and cysteine desulfurase activity, while the p.Pro591Ser and a previously described p.Arg776Cys variant in the C-terminal domain affect Molybdenum cofactor binding. Based on the results of haplotype analyses and historical genealogy findings, the potential dispersion of the identified variants is discussed. As far as we are aware, this is the largest cohort of xanthinuria cases described so far, substantially expanding the repertoire of pathogenic variants, characterizing structurally and functionally essential amino acid residues in the XDH and MOCOS proteins and addressing the population genetic aspects of classical xanthinuria.

Two type I restriction enzymes from Salmonella species

1985 ◽  
Vol 182 (4) ◽  
pp. 579-587 ◽  
Author(s):  
Valakunja Nagaraja ◽  
John C.W. Shepherd ◽  
Therese Pripfl ◽  
Thomas A. Bickle
Keyword(s):  
Restriction Enzymes ◽  
Type I

scholarly journals (E)-2-Methyl-6-{[(5-methylpyridin-2-yl)imino]methyl}phenol

IUCrData ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Md. Azharul Arafath ◽  
Farook Adam ◽  
Mohd. R. Razali
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Zigzag Chain ◽  
Aromatic Rings ◽  
Methyl Group ◽  
Compound C

In the title compound, C14H14N2O, the dihedral angle between the aromatic rings is 5.54 (9)°. The conformation is reinforced by an intramolecular O—H...N hydrogen bond, which closes anS(6) ring. The pyridine N atom and methyl group lie to opposite sides of the molecule. In the crystal, the molecules are linked into a zigzag chain propagating in [0-11] by weak C—H...O hydrogen bonds.

scholarly journals The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity

2009 ◽  
Vol 37 (20) ◽  
pp. 6960-6969 ◽  
Author(s):  
Nguyen To Uyen ◽  
Suk-Youl Park ◽  
Ji-Woo Choi ◽  
Hyun-Ju Lee ◽  
Kosuke Nishi ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
Vibrio Vulnificus ◽  
Type I ◽  
Dna Restriction

Mikrowellenspektrum, Hinderungspotential der internen Rotation und Dipolmoment des para-Fluortoluols

1965 ◽  
Vol 20 (12) ◽  
pp. 1682-1686 ◽  
Author(s):  
Heinz Dieter Rudolph ◽  
Helmut Seiler
Keyword(s):  
Dipole Moment ◽  
Internal Rotation ◽  
Absorption Lines ◽  
Type I ◽  
Rotational Spectrum ◽  
Rotation Barrier ◽  
Rotational Constants ◽  
Methyl Group ◽  
Microwave Rotational Spectrum ◽  
Internal Rotation Barrier

The microwave rotational spectrum of para-fluoro-toluene has been investigated in the region from 7 to 31 kmc/s. The three types of absorption lines to be expected in the case of a molecule of this type, i. e. with a very low sixfold barrier hindering the internal rotation of the methyl group, have been found: m=0, | m | ≠ 0, 3 n, | m | = 3 n. From the lines m=0 the rotational constants and the dipole moment, (1.96 ± 0.02) D, have been deduced; from the lines |m|=3 the internal rotation barrier could be calculated as V6=13.82 cal/mole. This V6 is compared with the values found for similar molecules.

Banding of rye (Secale cereale) chromosomes using the restriction enzymes AluI, DraI, HpaII, and MspI

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 998-1002 ◽  
Author(s):  
T. Stößer ◽  
T. Günther ◽  
C. U. Hesemann
Keyword(s):  
Secale Cereale ◽  
Restriction Enzymes ◽  
Chromosome Band ◽  
Banding Technique ◽  
Recognition Sequence ◽  
Metaphase Chromosomes ◽  
Banding Patterns ◽  
Secale Cereale L ◽  
Characteristic Banding

Mitotic metaphase chromosomes of the rye inbred line L 301, which belongs to the Sortiment of the University of Hohenheim, were treated in situ with the restriction enzymes AluI (recognition sequence: 5′-AC/GT-3′), DraI (recognition sequence: 5′-TTT/AAA-3′), and the isoschizomeres HpaII and MspI (recognition sequence: 5′-C/CGG-3′) and stained with Giemsa. The chromosomes indicated similar banding patterns in comparison with the conventional Giemsa-C-banding. However, we have found in rye chromosomes after restrictase treatment that the telomeric bands were reduced in extension. In a lower degree the centromeric bands of individual chromosomes could be absent in dependence of the used restriction enzymes. The number of the intercalary bands were also reduced. Nevertheless, the tested restriction enzymes produced characteristic banding patterns of the rye genome. This uncomplicated banding technique is suited for a very quick banding method of karyotype analysis especially to obtain a first survey of the band patterns on the rye chromosomes.Key words: Secale cereale L., chromosome band pattern, in situ digestion, restriction endonuclease, restriction banding.

scholarly journals Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

2000 ◽  
Vol 64 (2) ◽  
pp. 412-434 ◽  
Author(s):  
Noreen E. Murray
Keyword(s):  
Genetic Manipulation ◽  
Molecular Motor ◽  
Restriction Enzymes ◽  
Target Sequence ◽  
Type I ◽  
Dna Translocation ◽  
Chromosomal Dna ◽  
Dna Breakage ◽  
Intramolecular Communication ◽  
Alternative Activities

SUMMARY Restriction enzymes are well known as reagents widely used by molecular biologists for genetic manipulation and analysis, but these reagents represent only one class (type II) of a wider range of enzymes that recognize specific nucleotide sequences in DNA molecules and detect the provenance of the DNA on the basis of specific modifications to their target sequence. Type I restriction and modification (R-M) systems are complex; a single multifunctional enzyme can respond to the modification state of its target sequence with the alternative activities of modification or restriction. In the absence of DNA modification, a type I R-M enzyme behaves like a molecular motor, translocating vast stretches of DNA towards itself before eventually breaking the DNA molecule. These sophisticated enzymes are the focus of this review, which will emphasize those aspects that give insights into more general problems of molecular and microbial biology. Current molecular experiments explore target recognition, intramolecular communication, and enzyme activities, including DNA translocation. Type I R-M systems are notable for their ability to evolve new specificities, even in laboratory cultures. This observation raises the important question of how bacteria protect their chromosomes from destruction by newly acquired restriction specifities. Recent experiments demonstrate proteolytic mechanisms by which cells avoid DNA breakage by a type I R-M system whenever their chromosomal DNA acquires unmodified target sequences. Finally, the review will reflect the present impact of genomic sequences on a field that has previously derived information almost exclusively from the analysis of bacteria commonly studied in the laboratory.

scholarly journals Methyl (E)-2-({2-[(E)-(hydroxyimino)methyl]phenoxy}methyl)-3-(4-methylphenyl)acrylate

2012 ◽  
Vol 68 (6) ◽  
pp. o1617-o1617
Author(s):  
G. Ganesh ◽  
J. Srinivasan ◽  
E. Govindan ◽  
M. Bakthadoss ◽  
A. SubbiahPandi
Keyword(s):  
Double Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Crystal Packing ◽  
Aromatic Rings ◽  
Methyl Group ◽  
Compound C ◽  
Benzene Rings ◽  
The Mean ◽  
Centrosymmetric Dimers

In the title compound, C19H19NO4, the dihedral angle between the mean planes through the benzene rings is 82.18 (7)°. The C=N double bond is trans-configured. The molecules are linked into centrosymmetric dimers via pairs of O—H...N hydrogen bonds with the motif R 2 2(6). The crystal packing also features C—H...O interactions. The methyl group attached to one of the aromatic rings is disordered over two almost equally occupied positions [occpancy ratio = 0.51 (4):0.49 (4)].

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