scholarly journals An X-ray-crystallographic study of β-lactamase II from Bacillus cereus at 0.35 nm resolution

1987 ◽  
Vol 248 (1) ◽  
pp. 181-188 ◽  
Author(s):  
B J Sutton ◽  
P J Artymiuk ◽  
A E Cordero-Borboa ◽  
C Little ◽  
D C Phillips ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Metal Ion ◽  
Heavy Atom ◽  
Cysteine Residue ◽  
Histidine Residues ◽  
Glutamic Acid Residue ◽  
Cell Dimensions ◽  
Density Map ◽  
Beta Lactamase Ii ◽  
Electron Density Map

Crystals of beta-lactamase II (EC 3.5.2.6., ‘penicillinase’) from Bacillus cereus were grown with Cd(II) in place of the natural Zn(II) cofactor and stabilized by cross-linking with glutaraldehyde. Their space group is C2, the cell dimensions are a = 5.44 nm, b = 6.38 nm, c = 7.09 nm and beta = 93.6 degrees, and there is one molecule in the asymmetric unit. Diffraction data were collected from cross-linked crystals of the Cd(II)-enzyme, the apoenzyme and six heavy-atom derivatives. The electron-density map calculated at 0.35 nm resolution reveals the essential Cd(II) ion surrounded by three histidine residues and one cysteine residue. The position of a glutamic acid residue, modification of which destroys activity [Little, Emanuel, Gagnon & Waley (1986) Biochem. J. 233, 465-469], suggests the probable location of the active site of the enzyme. Two minor Cd(II) sites not essential for activity were also located. The structure of the apoenzyme at this resolution appears to differ from that of the Cd(II)-enzyme only in the orientation of two of the histidine residues and the cysteine residue that surround the metal ion.

scholarly journals Crystal structure of d(CCGGGGTACCCCGG)2at 1.4 Å resolution

2017 ◽  
Vol 73 (5) ◽  
pp. 259-265
Author(s):  
Selvam Karthik ◽  
Arunachalam Thirugnanasambandam ◽  
Pradeep Kumar Mandal ◽  
Namasivayam Gautham
Keyword(s):  
Crystal Structure ◽  
Metal Ion ◽  
Double Helix ◽  
Barium Chloride ◽  
Base Pairs ◽  
X Ray ◽  
Density Map ◽  
Solvent Molecules ◽  
Electron Density Map ◽  
Phosphate Groups

The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)2is reported at 1.4 Å resolution in the tetragonal space groupP41212. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA. A large number of solvent molecules have been identified in both the grooves of the duplex and around the backbone phosphate groups.

Crystallization and preliminary X-ray analysis of β-amylase from Bacillus polymyxa

1999 ◽  
Vol 55 (4) ◽  
pp. 898-900
Author(s):  
Takashi Yamane ◽  
Hiroshi Tasaki ◽  
Fusako Matsumoto ◽  
Atsuo Suzuki ◽  
Nobuyuki Uozumi ◽  
...  
Keyword(s):  
Diffusion Method ◽  
Bacillus Polymyxa ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Dimensions ◽  
Protein Molecules ◽  
Density Map ◽  
Electron Density Map

A truncated β-amylase (E.C. 3.2.1.2) from Bacillus polymyxa has been crystallized using the hanging-drop vapour-diffusion method at 277 K. The crystals belong to the orthorhombic space group P212121 with cell dimensions a = 64.6, b = 141.9, c = 155.1 Å and diffract to 2.5 Å resolution. The asymmetric unit containing three protein molecules was derived from an electron-density map calculated at 4 Å resolution using MIR phases. This gives a Vm value of 2.36 Å3 Da−1.

Macromolecular phasing with SHELXE

2002 ◽  
Vol 217 (12) ◽  
Author(s):  
G. M. Sheldrick
Keyword(s):  
Electron Density ◽  
Heavy Atom ◽  
Small Contribution ◽  
Initial Electron ◽  
Density Map ◽  
Electron Density Map

AbstractSHELXE was designed to provide a simple, fast and robust route from substructure sites found by the program SHELXD to an initial electron density map, if possible with an indication as to which heavy-atom enantiomorph is correct. This should be understood as a small contribution to

scholarly journals A thiono-β-lactam substrate for the β-lactamase II of Bacillus cereus. Evidence for direct interaction between the essential metal ion and substrate

1989 ◽  
Vol 258 (3) ◽  
pp. 765-768 ◽  
Author(s):  
B P Murphy ◽  
R F Pratt
Keyword(s):  
Bacillus Cereus ◽  
Active Site ◽  
Metal Ion ◽  
Direct Interaction ◽  
Beta Lactamase ◽  
Beta Lactam ◽  
Enzyme Active Site ◽  
Lactam Carbonyl ◽  
Beta Lactamase Ii ◽  
Hydrolysis Of

An 8-thionocephalosporin was shown to be a substrate of the beta-lactamase II of Bacillus cereus, a zinc metalloenzyme. Although it is a poorer substrate, as judged by the Kcat./Km parameter, than the corresponding 8-oxocephalosporin, the discrimination against sulphur decreased when the bivalent metal ion in the enzyme active site was varied in the order Mn2+ (the manganese enzyme catalysed the hydrolysis of the oxo compound but not that of the thiono compound), Zn2+, Co2+ and Cd2+. This result is taken as evidence for kinetically significant direct contact between the active-site metal ion of beta-lactamase II and the beta-lactam carbonyl heteroatom. No evidence was obtained, however, for accumulation of an intermediate with such co-ordination present.

Automatic procedure for crystal-structure analysis with the heavy-atom technique*

1971 ◽  
Vol 134 (1-2) ◽  
Author(s):  
Vasantha Pattabhi ◽  
K. Venkatesan
Keyword(s):  
Electron Density ◽  
Least Squares Method ◽  
Heavy Atom ◽  
Site Occupancy ◽  
Crystal Structure Analysis ◽  
Density Maps ◽  
Structure Factors ◽  
Subsequent Calculation ◽  
Density Map ◽  
Electron Density Map

AbstractThis paper deals with a possible method of determining molecular structure directly, using x-ray data. The peaks chosen from the electron-density map calculated using the signs obtained from the contribution of the heavy atom are assigned site-occupancy values which depend upon the peak heights. The occupancy parameter is refined by the least-squares method and the peaks for which the value of the occupancy parameters increases are taken as real atoms in the subsequent calculation of structure factors and electron-density maps. The method has been tested in two hypothetical cases and in a real case.

scholarly journals Identification of histidine residues that act as zinc ligands in β-lactamase II by differential tritium exchange

1979 ◽  
Vol 179 (3) ◽  
pp. 459-463 ◽  
Author(s):  
G S Baldwin ◽  
S G Waley ◽  
E P Abraham
Keyword(s):  
Bacillus Cereus ◽  
Binding Site ◽  
Beta Lactamase ◽  
Histidine Residues ◽  
Tryptic Digest ◽  
Beta Lactamase Ii

1. Four histidine-containing peptides have been isolated from a tryptic digest of the Zn2+-requiring beta-lactamase II from Bacillus cereus. One of these peptides probably contains two histidine residues. 2. The presence of one equivalent of Zn2+ substantially decreases the rate of exchange of the C-2 proton in at least two and probably three of the histidine residues of these peptides for solvent 3H. 3. It is concluded that peptides containing at least two of the three histidine residues acting as Zn2+ ligands at the tighter Zn2+-binding site of beta-lactamase II have been identified.

scholarly journals Identification of an essential glutamic acid residue in β-lactamase II from Bacillus cereus

1986 ◽  
Vol 233 (2) ◽  
pp. 465-469 ◽  
Author(s):  
C Little ◽  
E L Emanuel ◽  
J Gagnon ◽  
S G Waley
Keyword(s):  
Glutamic Acid ◽  
Bacillus Cereus ◽  
Gel Filtration ◽  
Thiol Group ◽  
Water Soluble ◽  
Beta Lactamase ◽  
Pepsin Digestion ◽  
Early Stages ◽  
Glutamic Acid Residue ◽  
Beta Lactamase Ii

Beta-Lactamase II from Bacillus cereus was readily inactivated by incubation at pH 4.75 with a water-soluble carbodiimide plus a suitable nucleophile. In the early stages of the reaction, 1 equivalent of nucleophile was incorporated/equivalent of enzyme, whereas during the later stages a second equivalent of nucleophile was also incorporated. This latter process correlated with the blocking of the enzyme's single thiol group. Enzyme inactivated in the presence of the coloured nucleophile N-(2,4-dinitrophenyl)ethylenediamine was fragmented by pepsin digestion, and coloured peptides were isolated by gel filtration and h.p.l.c. Two major peptides, representing 52% of the incorporated label, were isolated and sequenced. Both peptides contained the incorporated label on glutamic acid-37, and it is concluded that this latter residue represents a catalytically essential carboxylic residue in beta-lactamase II.

The 4.5 Å Resolution Structure of a Bacterial Serine Protease from Streptomyces Griseus

1974 ◽  
Vol 52 (3) ◽  
pp. 208-220 ◽  
Author(s):  
P. W. Codding ◽  
L. T. J. Delbaere ◽  
K. Hayakawa ◽  
W. L. B. Hutcheon ◽  
M. N. G. James ◽  
...  
Keyword(s):  
Electron Density ◽  
Streptomyces Griseus ◽  
Protein Mass ◽  
Isomorphous Replacement ◽  
Resolution Electron ◽  
Cell Dimensions ◽  
Metal Derivatives ◽  
Density Map ◽  
Unit Cell Dimensions ◽  
Electron Density Map

Three crystalline modifications of the bacterial serine peptidase Streptomyces griseus Protease B have been grown. A 4.5 Å resolution electron density map of one form has been computed from the multiple isomorphous replacement (MIR) phases deduced from two heavy metal derivatives plus the anomalous dispersion effects of one of the derivatives. The crystalline modification used was grown from 0.7–1.0 M KH2PO4 at pH 4.2. These crystals have space group P21212 and unit cell dimensions of a = 44.15 (5) Å, b = 108.72 (10) Å, and c = 37.28 (5) Å. The crystal asymmetric unit contains a protein mass of approximately 19 000 daltons. The electron density map, mean figure of merit 0.80, clearly shows the molecular boundary; relatively long stretches of extended chain are discernable. The active site has been identified from a difference electron density map computed using the MIR protein phases and the amplitude differences between a crystal of the enzyme inhibited at the active serine in solution by p-iodobenzenesulfonyl fluoride (PIPSYL) and those from a crystal of the native enzyme. In addition to showing the site of the PIPSYL binding, there is an apparent conformational change in which the histidine side chain moves away from the serine residue by approximately 4.3 Å.

The low-resolution structure of human muscle aldolase

1981 ◽  
Vol 293 (1063) ◽  
pp. 209-214 ◽  
Keyword(s):  
Domain Structure ◽  
Electron Density ◽  
Heavy Atom ◽  
Three Dimensional ◽  
Human Muscle ◽  
Dimensional Structure ◽  
Density Map ◽  
Electron Density Map ◽  
Spherical Molecule ◽  
Resolution Structure

The three-dimensional structure of human muscle aldolase has been solved at 5 A resolution with the use of two isomorphous heavy atom derivatives. The enzyme’s four subunits are arranged about three mutually perpendicular intersecting twofold axes to form a compact spherical molecule. The subunit boundaries are clearly defined but a possible domain structure is not apparent in this preliminary electron density map.

X-ray structural studies of Rubisco from Rhodospirillum rubrum and spinach

1986 ◽  
Vol 313 (1162) ◽  
pp. 359-365 ◽  
Keyword(s):  
Pyridoxal Phosphate ◽  
Rhodospirillum Rubrum ◽  
Heavy Atom ◽  
Small Subunit ◽  
Monoclinic Space Group ◽  
Orthorhombic Crystal ◽  
Dimeric Molecule ◽  
Large Hole ◽  
Cell Dimensions ◽  
Electron Density Map

An electron density map to 2.9 Å (1 Å = 10 -10 m) resolution of Rubisco from Rhodospirillum rubrum has been obtained from crystals of the gene product expressed in Escherichia coli . These crystals are monoclinic, space group P2 1 with cell dimensions a = 65.5 Å, b = 70.6 Å, c = 104.1 Å and β = 92° and with two subunits per asymmetric unit. Isomorphous phases were obtained from three heavy atom derivatives. The dimeric molecule has the shape of a distorted ellipsoid with approximate dimensions 45 x 70 x 105 Å. The subunit interactions in the dimeric molecule are tight and extensive. Each subunit is divided into two main domains, one of which has extensive α/β structure probably folded into the common eight unit barrel structure. NADPH and pyridoxal phosphate bind at one end of this domain in each subunit. Two different octameric molecules with approximate (422) symmetry have been constructed from the L 2 dimeric molecule from R. rubrum , assuming that the molecular twofold axis of the L 2 dimer is preserved in the L 8 molecule. It is shown that only one of these is compatible with the orthorhombic crystal lattice of spinach and Alcaligenes eutrophus Rubisco. The L 8 molecule thus obtained is ellipsoidal with approximate dimensions 130 Å x 130 Å x 105 Å and with a large hole in the middle of about 40 Å diameter around the fourfold axis. A cleft in each subunit between the two domains could form a binding site for the small subunit in the plant L 8 S 8 Rubisco molecule.

Sign in / Sign up

Export Citation Format

Share Document