scholarly journals Structure-function relationships in the cysteine proteinases actinidin, papain and papaya proteinase Ω. Three-dimensional structure of papaya proteinase Ω deduced by knowledge-based modelling and active-centre characteristics determined by two-hydronic-state reactivity probe kinetics and kinetics of catalysis

1991 ◽  
Vol 280 (1) ◽  
pp. 79-92 ◽  
Author(s):  
C M Topham ◽  
E Salih ◽  
C Frazao ◽  
D Kowlessur ◽  
J P Overington ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Catalytic Site ◽  
The Other ◽  
Dimensional Structure ◽  
Cysteine Proteinases ◽  
Three Dimensional Structure ◽  
Knowledge Based ◽  
Thiol Reactivity ◽  
Ph Dependent ◽  
Kinetics Of

1. A model of the three-dimensional structure of papaya proteinase omega, the most basic cysteine proteinase component of the latex of papaya (Carica papaya), was built from its amino acid sequence and the two currently known high-resolution crystal structures of the homologous enzymes papain (EC 3.4.22.2) and actinidin (EC 3.4.22.14). The method used a knowledge-based approach incorporated in the COMPOSER suite of programs and refinement by using the interactive graphics program FRODO on an Evans and Sutherland PS 390 and by energy minimization using the GROMOS program library. 2. Functional similarities and differences between the three cysteine proteinases revealed by analysis of pH-dependent kinetics of the acylation process of the catalytic act and of the reactions of the enzyme catalytic sites with substrate-derived 2-pyridyl disulphides as two-hydronic-state reactivity probes are reported and discussed in terms of the knowledge-based model. 3. To facilitate analysis of complex pH-dependent kinetic data, a multitasking application program (SKETCHER) for parameter estimation by interactive manipulation of calculated curves and a simple method of writing down pH-dependent kinetic equations for reactions involving any number of reactive hydronic states by using information matrices were developed. 4. Papaya proteinase omega differs from the other two enzymes in the ionization characteristics of the common (Cys)-SH/(His)-Im+H catalytic-site system and of the other acid/base groups that modulate thiol reactivity towards substrate-derived inhibitors and the acylation process of the catalytic act. The most marked difference in the Cys/His system is that the pKa for the loss of the ion-pair state to form -S-/-Im is 8.1-8.3 for papaya proteinase omega, whereas it is 9.5 for both actinidin and papain. Papaya proteinase omega is similar to actinidin in that it lacks the second catalytically influential group with pKa approx. 4 present in papain and possesses a catalytically influential group with pKa 5.5-6.0. 5. Papaya proteinase omega occupies an intermediate position between actinidin and papain in the sensitivity with which hydrophobic interaction in the S2 subsite is transmitted to produce changes in transition-state geometry in the catalytic site, a fact that may be linked with differences in specificity in P2-S2 interaction exhibited by the three enzymes.(ABSTRACT TRUNCATED AT 400 WORDS)

scholarly journals Bis(μ2-4-nitrophenolato)bis(4-nitrophenolato)di-μ3-oxido-octaphenyltetratin chloroform sesquisolvate [+ solvate]: a tetranuclear stannoxane

IUCrData ◽  
2019 ◽  
Vol 4 (8) ◽  
Author(s):  
Patrick Butler
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Coordination Geometry ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Complex Molecules ◽  
Three Dimensional Structure

The title tetranuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex molecules, A and B, in the asymmetric unit together with 1.5 molecules of chloroform. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex molecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex molecules are linked by a number of C—H...O hydrogen bonds within the layers and between the layers, forming a supramolecular three-dimensional structure.

scholarly journals Synthesis and crystallographic characterization of a mononuclear cobalt(III) complex possessing both thiolate and thioether donors: reactivity of an thiolate-bridged pentanuclear Co2Ag3complex with iodomethane

2017 ◽  
Vol 73 (5) ◽  
pp. 678-681
Author(s):  
Yosuke Fukuda ◽  
Nobuto Yoshinari ◽  
Takumi Konno
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Mononuclear Complex ◽  
The Other ◽  
Dimensional Structure ◽  
Cationic Complex ◽  
Three Dimensional Structure ◽  
Mononuclear Cobalt

Treatment of an S-bridged pentanuclear AgI3CoIII2complex, [Ag3{Co(L)}2]3+[L3–= N(CH2NHCH2CH2S−)3], in which two tris(thiolate)-type mononuclear CoIIIunits ([Co(L)]) are bridged by three AgIions through S atoms, with iodomethane (CH3I) gave a new CoIIImononuclear complex, [Co(LMe2)]2+[LMe2−= N(CH2NHCH2CH2S−)(CH2NHCH2CH2SCH3)2], systematic name: {2-[(bis{[2-(methylsulfanyl)ethyl]aminomethyl}aminomethyl)amino]ethanethiolato}cobalt(III) bis(hexafluoridophosphate). This cationic complex was crystallized with PF6−anions to form the title compound, [Co(LMe2)](PF6)2. In the [Co(LMe2)]2+cation, two of three thiolate groups in [Co(L)] are methylated while one thiolate group remains unreacted. Although a total of eight stereoisomers are possible for [Co(LMe2)]2+, only a pair of enantiomers {ΛRR- and ΔSS-[Co(LMe2)]2+} are selectively formed. In the crystal, the complex cations and the PF6−anions are connected through weak N—H...F, C—H...F and C—H...S hydrogen bonds into a three-dimensional structure. Two F atoms in one PF6anion are disordered over two sets of sites with refined occupancies of 0.61 (4) and 0.39 (4) and two F atoms in the other PF6−anion are disordered over two sets of sites with occupancies of 0.5.

scholarly journals Structural Study of the Serratia entomophila Antifeeding Prophage: Three-Dimensional Structure of the Helical Sheath

2010 ◽  
Vol 192 (17) ◽  
pp. 4522-4525 ◽  
Author(s):  
Anindito Sen ◽  
Daria Rybakova ◽  
Mark R. H. Hurst ◽  
Alok K. Mitra
Keyword(s):  
Electron Microscopy ◽  
Image Processing ◽  
New Zealand ◽  
Structural Study ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Costelytra Zealandica

ABSTRACT The sheath of the Serratia entomophila antifeeding prophage, which is pathogenic to the New Zealand grass grub Costelytra zealandica, is a 3-fold helix formed by a 4-fold symmetric repeating motif disposed around a helical inner tube. This structure, determined by electron microscopy and image processing, is distinct from that of the other known morphologically similar bacteriophage sheaths.

scholarly journals Three-dimensional reconstruction of a simple Z-band in fish muscle.

1991 ◽  
Vol 113 (5) ◽  
pp. 1043-1055 ◽  
Author(s):  
P K Luther
Keyword(s):  
Actin Filament ◽  
Actin Filaments ◽  
Rotational Symmetry ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Central Plane ◽  
Three Dimensional Structure ◽  
Proximal Site ◽  
Distal Site

The three-dimensional structure of the Z-band in fish white muscle has been investigated by electron microscopy. This Z-band is described as simple, since in longitudinal sections it has the appearance of a single zigzag pattern connecting the ends of actin filaments of opposite polarity from adjacent sarcomeres. The reconstruction shows two pairs of links, the Z-links, between one actin filament and the facing four actin filaments in the adjacent sarcomere. The members of each pair have nearly diametrically opposed origins. In relation to one actin filament, one pair of links appears to bind along the final 10 nm of the actin filament (proximal site) and the other pair binds along a region extending from 5 to 20 nm from the filament end (distal site). Between one pair and the other, there is a rotation of approximately 80 degrees round the filament axis. A Z-link with a proximal site at the end of one actin filament attaches at a distal site on the oppositely oriented actin filaments of the facing sarcomere and vice versa. The length of each Z-link is consistent with the length of an alpha-actinin molecule. An additional set of links located 10-15 nm from the center of the Z-band occurs between actin filaments of the same polarity. These polar links connect the actin filaments along the same direction on each side of the Z-band. The three-dimensional structure appears to have twofold screw symmetry about the central plane of the Z-band. Only approximate twofold rotational symmetry is observed in directions parallel to the actin filaments. Previous models of the Z-band in which four identical and rotationally symmetrical links emanate from the end of one actin filament and span across to the ends of four actin filaments in the adjacent sarcomere are therefore incorrect.

Three-dimensional structure and thiol reactivity characteristics of chymopapain M (papaya proteinase IV)

1990 ◽  
Vol 18 (5) ◽  
pp. 934-935 ◽  
Author(s):  
CHRISTOPHER M. TOPHAM ◽  
JOHN OVERINGTON ◽  
MARK THOMAS ◽  
DEVANAND KOWLESSUR ◽  
EMRYS W. THOMAS ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Thiol Reactivity

scholarly journals Structure of a Coenzyme A Pyrophosphatase from Deinococcus radiodurans: a Member of the Nudix Family

2003 ◽  
Vol 185 (14) ◽  
pp. 4110-4118 ◽  
Author(s):  
Lin-Woo Kang ◽  
Sandra B. Gabelli ◽  
Mario A. Bianchet ◽  
Wen Lian Xu ◽  
Maurice J. Bessman ◽  
...  
Keyword(s):  
Binding Site ◽  
Coenzyme A ◽  
Deinococcus Radiodurans ◽  
Substrate Binding ◽  
Three Dimensional ◽  
Catalytic Site ◽  
Dimensional Structure ◽  
Nudix Hydrolase ◽  
Three Dimensional Structure ◽  
Sequence Characteristic

ABSTRACT Gene Dr1184 from Deinococcus radiodurans codes for a Nudix enzyme (DR-CoAse) that hydrolyzes the pyrophosphate moiety of coenzyme A (CoA). Nudix enzymes with the same specificity have been found in yeast, humans, and mice. The three-dimensional structure of DR-CoAse, the first of a Nudix hydrolase with this specificity, reveals that this enzyme contains, in addition to the fold observed in other Nudix enzymes, insertions that are characteristic of a CoA-hydrolyzing Nudix subfamily. The structure of the complex of the enzyme with Mg2+, its activating cation, reveals the position of the catalytic site. A helix, part of the N-terminal insertion, partially occludes the binding site and has to change its position to permit substrate binding. Comparison of the structure of DR-CoAse to those of other Nudix enzymes, together with the location in the structure of the sequence characteristic of CoAses, suggests a mode of binding of the substrate to the enzyme that is compatible with all available data.

scholarly journals Poly[bis(μ6-benzene-1,3,5-tricarboxylato-κ7 O 1,O 1′:O 1′:O 3:O 3′:O 5:O 5′)tetrakis(dimethylformamide-κO)trimagnesium(II)]

2012 ◽  
Vol 68 (6) ◽  
pp. m852-m853
Author(s):  
Katarzyna Łuczyńska-Szymczak ◽  
Wojciech Starosta ◽  
Janusz Leciejewicz
Keyword(s):  
Title Compound ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Asymmetric Unit ◽  
Three Dimensional Structure

The asymmetric unit of the polymeric title compound, [Mg3(C9H3O6)2(C3H7NO)4] n , contains three MgII ions bridged by carboxylate O atoms from two fully deprotonated benzene-1,3,5-tricarboxylate (BTC) trianions and four metal-coordinated dimethylformamide (DMF) molecules. One MgII ion is octahedrally coordinated by six carboxylate O atoms. The other two cations are each octahedrally coordinated by four carboxylate O atoms and two O atoms donated by two DMF molecules: in one, the DMF molecules are cis and in the other they are trans. The three MgII octahedra form clusters, which are bridged by the BTC trianions, generating a three-dimensional structure.

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