A comparative study on .alpha.-glucan phosphorylases from plant and animal: interrelationship between the polysaccharide and pyridoxal phosphate binding sites by affinity electrophoresis

Biochemistry ◽  
1980 ◽  
Vol 19 (11) ◽  
pp. 2287-2294 ◽  
Author(s):  
Shoji Shimomura ◽  
Toshio Fukui
Keyword(s):  
Comparative Study ◽  
Binding Sites ◽  
Pyridoxal Phosphate ◽  
Phosphate Binding ◽  
Affinity Electrophoresis

scholarly journals Pyridoxal Phosphate Binding Sites Are Similar in Human Heme-dependent and Yeast Heme-independent Cystathionine β-Synthases

2001 ◽  
Vol 276 (22) ◽  
pp. 19350-19355 ◽  
Author(s):  
Ömer Kabil ◽  
Shinichi Toaka ◽  
Russell LoBrutto ◽  
Richard Shoemaker ◽  
Ruma Banerjee
Keyword(s):  
Binding Sites ◽  
Pyridoxal Phosphate ◽  
Phosphate Binding

Analysis of the surface topography of glycogen phosphorylase a: implications for metabolic interconversion and regulatory mechanisms

1979 ◽  
Vol 57 (6) ◽  
pp. 789-797 ◽  
Author(s):  
R. J. Fletterick ◽  
S. Sprang ◽  
N. B. Madsen
Keyword(s):  
Surface Topography ◽  
Conformational Changes ◽  
Binding Sites ◽  
Pyridoxal Phosphate ◽  
Glycogen Storage ◽  
Enzymic Activity ◽  
Phosphate Binding ◽  
Active Centers ◽  
Large Molecular Weight ◽  
T State

Computer drawings of the van der Waals contours of atoms on the surface represent the phosphorylase molecule at 2.5 Å (1 Å = 0.1 nm) resolution with color coding for acidic and basic residues, bound ligands, or conformational changes. The asymmetry resulting from the twofold axis of each dimer provides two faces which can be distinguished structurally and functionally. Thus, a concave catalytic face contains the glycogen storage sites on its periphery with entrances to the glucose-1-phosphate binding sites of the active centers, adjacent to the pyridoxal phosphate moieties, near its center. Just outside the active site is a binding site for negative effectors such as caffeine. On the side of the dimer opposite to the catalytic face is found a convex control face containing the binding sites for the allosteric activator AMP, for which ATP also competes. Quite close to these sites are found the Ser-14-phosphates hydrogen bonded to Arg-69 and Arg-43′ of the symmetry-related monomer. Each Ser-14-phosphate is surrounded by positive charges, including more than are found on adjacent sequences, and therefore, comparative studies on peptides cannot describe fully the specificity and binding requirements of the kinase and phosphatase.The surface topography of the glucose stabilized T state (taut) and the changes which occur during the allosteric transitions induced by AMP and substrates are discussed in terms of their functional implications for the control of both the intrinsic enzymic activity and of the metabolic interconversions between the a and b forms. In particular, the two conformational states (taut and relaxed) exhibit different structural arrangements of the binding sites for the negative effector, caffeine, and the positive effector, AMP. Linkage between the various effector sites is demonstrated by conformational changes in the surface topography. Since the control face is opposite to the catalytic face, the interconverting enzymes can bind to, and act on, the phosphorylase while the latter is bound to glycogen. The Ser-14 residues are only 40 Å apart across the control face and could be bridged readily by the multimeric kinase (α4β4γ4δ4, 1 300 000 daltons) or the large molecular weight form of the phosphatase. The T →R conformational change causes the Ser-14-phosphate to move 5 Å in from the surface, which may be related to the 20-fold decrease of the phosphatase Vm with unchanged Km.

Specification of the bonding cavities available in metal-binding sites: a comparative study of a series of quadridentate macrocyclic ligands

1984 ◽  
Vol 106 (6) ◽  
pp. 1641-1645 ◽  
Author(s):  
Kim Henrick ◽  
Leonard F. Lindoy ◽  
Mary McPartlin ◽  
Peter A. Tasker ◽  
Michael P. Wood
Keyword(s):  
Comparative Study ◽  
Metal Binding ◽  
Binding Sites ◽  
Macrocyclic Ligands ◽  
Metal Binding Sites

scholarly journals Gene Cloning and Molecular Characterization of Lysine Decarboxylase from Selenomonas ruminantiumDelineate Its Evolutionary Relationship to Ornithine Decarboxylases from Eukaryotes

2000 ◽  
Vol 182 (23) ◽  
pp. 6732-6741 ◽  
Author(s):  
Yumiko Takatsuka ◽  
Yoshihiro Yamaguchi ◽  
Minenobu Ono ◽  
Yoshiyuki Kamio
Keyword(s):  
Amino Acid ◽  
Substrate Specificity ◽  
Pyridoxal Phosphate ◽  
Evolutionary Relationship ◽  
Binding Domain ◽  
Sequencing Analysis ◽  
Lysine Decarboxylase ◽  
Amino Acid Residues ◽  
Phosphate Binding ◽  
Link Type

ABSTRACT Lysine decarboxylase (LDC; EC 4.1.1.18 ) from Selenomonas ruminantium comprises two identical monomeric subunits of 43 kDa and has decarboxylating activities toward both l-lysine andl-ornithine with similar Km andVmax values (Y. Takatsuka, M. Onoda, T. Sugiyama, K. Muramoto, T. Tomita, and Y. Kamio, Biosci. Biotechnol. Biochem. 62:1063–1069, 1999). Here, the LDC-encoding gene (ldc) of this bacterium was cloned and characterized. DNA sequencing analysis revealed that the amino acid sequence of S. ruminantium LDC is 35% identical to those of eukaryotic ornithine decarboxylases (ODCs; EC 4.1.1.17 ), including the mouse,Saccharomyces cerevisiae, Neurospora crassa,Trypanosoma brucei, and Caenorhabditis elegansenzymes. In addition, 26 amino acid residues, K69, D88, E94, D134, R154, K169, H197, D233, G235, G236, G237, F238, E274, G276, R277, Y278, K294, Y323, Y331, D332, C360, D361, D364, G387, Y389, and F397 (mouse ODC numbering), all of which are implicated in the formation of the pyridoxal phosphate-binding domain and the substrate-binding domain and in dimer stabilization with the eukaryotic ODCs, were also conserved inS. ruminantium LDC. Computer analysis of the putative secondary structure of S. ruminantium LDC showed that it is approximately 70% identical to that of mouse ODC. We identified five amino acid residues, A44, G45, V46, P54, and S322, within the LDC catalytic domain that confer decarboxylase activities toward bothl-lysine and l-ornithine with a substrate specificity ratio of 0.83 (defined as thek cat/Km ratio obtained with l-ornithine relative to that obtained withl-lysine). We have succeeded in converting S. ruminantium LDC to form with a substrate specificity ratio of 58 (70 times that of wild-type LDC) by constructing a mutant protein, A44V/G45T/V46P/P54D/S322A. In this study, we also showed that G350 is a crucial residue for stabilization of the dimer in S. ruminantium LDC.

Distinct localization of atrial natriuretic factor and angiotensin II binding sites in the glomerulus

1986 ◽  
Vol 251 (4) ◽  
pp. F594-F602 ◽  
Author(s):  
C. Bianchi ◽  
J. Gutkowska ◽  
G. Thibault ◽  
R. Garcia ◽  
J. Genest ◽  
...  
Keyword(s):  
Angiotensin Ii ◽  
Comparative Study ◽  
Binding Sites ◽  
Atrial Natriuretic Factor ◽  
Mesangial Cells ◽  
Ang Ii ◽  
Half Maximum ◽  
Natriuretic Factor ◽  
Glomerular Size ◽  
Atrial Natriuretic

A comparative study of the localization of 125I-labeled atrial natriuretic factor (ANF) and 125I-labeled angiotensin II (ANG II) binding sites in the glomerulus of the rat, after an intravascular injection, has been done by ultrastructural radioautography. 125I-ANF binding sites are localized predominantly on the podocytes of the visceral epithelium (63%) followed by the endothelium of capillaries (14%), the parietal epithelium (13%), and finally mesangial cells (10%). In a comparative study, it was confirmed that 125I-ANG II uptake is localized predominantly on mesangial cells (60%) followed by epithelial visceral cells (23%) and the endothelium of capillaries (16%). Using isolated rat glomeruli, it was confirmed that ANG II decreases glomerular size (maximum effect of 15%) with an apparent half maximum effective concentration (EC50) between 10(-9) and 10(-8) M. Although ANF alone has no apparent effect on glomerular size, it inhibits the contractile effect of ANG II with a half maximum inhibitory concentration (IC50) between 10(-11) and 10(-10) M. These results suggest that an intraglomerular mechanism other than glomerular arteriolar resistance may be involved in the modulation of glomerular filtration rate by ANF. The presence of 125I-ANF uptake mainly in foot processes of visceral epithelial cells of glomeruli in vivo and the inhibition of ANG II decrease in glomerular size by ANF in vitro raise the possibility that ANF may regulate the ultrafiltration coefficient by two mechanisms: modulation of glomerular permeability, and surface area.

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