The crystal structure of spermidine trihydrochloride

Giglio, E.; Liquori, A. M.; Puliti, R.; Ripamonti, A.

doi:10.1107/s0365110x66001609

Cited by 12 publications

(9 citation statements)

References 2 publications

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“…The significant differences detected, for the same temperature, from putrescine dihydrochloride to spermine tetrahydrochloride are clear evidence of the effect of both the polyamine chain length and the number of amine/imine groups on the conformational behaviour of these molecules. In fact, this is in close accord with the x-ray data reported in the literature, 42 which indicate an extended all-trans geometry for the polyamines under study, and only a slightly twisted orientation (one gauche tilt) for the hydrochloride form of the tetraamine spermine.…”

Section: And (C) Vs (B) and (D)]supporting

confidence: 81%

Raman spectra of putrescine, spermidine and spermine polyamines and their N‐deuterated and N‐ionized derivatives

Costa¹,

Marques²,

Carvalho³

2003

J Raman Spectroscopy

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The experimental and calculated Raman spectra of the N-hydrogenated and N-deuterated biogenic polyamines putrescine, spermidine and spermine and of their N-hydrogenated and N-deuterated hydrochloride salts in the 2000-3400 cm −1 spectral region (at distinct temperatures) are reported and analysed. A complete assignment of the N-H, C-H and N-D stretching modes is carried out, in the light of both steric and hydrogen-bonding interactions on the conformational behaviour of these systems.

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Section: And (C) Vs (B) and (D)]supporting

confidence: 81%

Raman spectra of putrescine, spermidine and spermine polyamines and their N‐deuterated and N‐ionized derivatives

Costa¹,

Marques²,

Carvalho³

2003

J Raman Spectroscopy

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“…The same densities have been found within all four molecules in the asymmetric unit, indicating that the bound spermidine molecules adopt the identical conformation. Interestingly, the spermidine molecule is bent within the PotD molecule, whereas all kinds of the crystal structures of spermidine in the Cambridge structural data base exhibit a linear shape (33,34).…”

Section: Refinement Statisticsmentioning

confidence: 97%

Crystal Structure of PotD, the Primary Receptor of the Polyamine Transport System in Escherichia coli

Sugiyama

Vassylyev

Matsushima

et al. 1996

Journal of Biological Chemistry

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PotD protein is a periplasmic binding protein and the primary receptor of the polyamine transport system, which regulates the polyamine content in Escherichia coli. The crystal structure of PotD in complex with spermidine has been solved at 2.5-A resolution. The PotD protein consists of two domains with an alternating beta-alpha-beta topology. The polyamine binding site is in a central cleft lying in the interface between the domains. In the cleft, four acidic residues recognize the three positively charged nitrogen atoms of spermidine, while five aromatic side chains anchor the methylene backbone by van der Waals interactions. The overall fold of PotD is similar to that of other periplasmic binding proteins, and in particular to the maltodextrin-binding protein from E. coli, despite the fact that sequence identity is as low as 20%. The comparison of the PotD structure with the two maltodextrin-binding protein structures, determined in the presence and absence of the substrate, suggests that spermidine binding rearranges the relative orientation of the PotD domains to create a more compact structure.

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“…The crystal structure of the free spermidine molecule has already been determined by two groups (Giglio et al, 1966;Huse & Iitaka, 1969). We compared these structures with the 1.8-A structure of spermidine bound to PotD (Fig.…”

Section: Spermidine Bindingmentioning

confidence: 99%

“…Substitution of Ala 182 may cause PotF to lose this strong electrostatic interaction with spermidine, and hence it decreases its ability to bind spermidine. In the PotD protein, the side Giglio et al (1966). Huse and Iitaka (1969).…”

Section: Substrate Specificity Of Polyamine-binding Proteinsmentioning

confidence: 99%

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The 1.8‐Å X‐ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding

et al. 1996

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The PotD protein from Escherichia coli is one of the components of the polyamine transport system present in the periplasm. This component specifically binds either spermidine or putrescine. The crystal structure of the E. coli PotD protein complexed with spermidine was solved at 1.8 8, resolution and revealed the detailed substrate-binding mechanism. The structure provided the detailed conformation of the bound spermidine. Furthermore, a water molecule was clearly identified in the binding site lying between the amino-terminal domain and carboxyl-terminal domain. Through this water molecule, the bound spermidine molecule forms two hydrogen bonds with Thr 35 and Ser 21 1. Another periplasmic component of polyamine transport, the PotF protein, exhibits 35% sequence identity with the PotD protein, and it binds only putrescine, not spermidine. To understand these different substrate specificities, model building of the PotF protein was performed on the basis of the PotD crystal structure. The hypothetical structure suggests that the side chain of Lys 349 in PotF inhibits spermidine binding because of the repulsive forces between its positive charge and spermidine. On the other hand, putrescine could be accommodated into the binding site without any steric hindrance because its molecular size is much smaller than that of spermidine, and the positively charged amino group is relatively distant from Lys 349.

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The crystal structure of spermidine trihydrochloride

Cited by 12 publications

References 2 publications

Raman spectra of putrescine, spermidine and spermine polyamines and their N‐deuterated and N‐ionized derivatives

Raman spectra of putrescine, spermidine and spermine polyamines and their N‐deuterated and N‐ionized derivatives

Crystal Structure of PotD, the Primary Receptor of the Polyamine Transport System in Escherichia coli

The 1.8‐Å X‐ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding

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