Structural studies of type I DNA topoisomerases

The shape of the cross section of a dense fiber bundle is related to the symmetry of its molecular packing. However, this statement might be belied by type I collagen fibrils which have a rounded section of high symmetry while structural studies suggest that their molecules are assembled with a long range lateral order of lower symmetry. We examine how phyllotaxis, which is a nonconventional crystallographic solution to packing efficiency in situations of high radial symmetry, can establish a link between those two apparently conflicting points. The lateral order imposed by the algorithm of phyllotaxis, which implies an enlargement of the notion of long range lateral order beyond that used for classical crystals, provides a basis for a new analysis of the experimental data.

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Structural studies of type I topoisomerases

Nucleic Acids Research ◽

10.1093/nar/gkn1009 ◽

2008 ◽

Vol 37 (3) ◽

pp. 693-701 ◽

Cited By ~ 65

Author(s):

N. M. Baker ◽

R. Rajan ◽

A. Mondragon

Keyword(s):

Type I ◽

Structural Studies ◽

Type I Topoisomerases

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Biosynthetic and Structural Studies of Hemoglobin in a Patient with Congenital Dyserythropoietic Anemia Type I

Hemoglobin ◽

10.3109/03630267708999173 ◽

1977 ◽

Vol 1 (7) ◽

pp. 663-677 ◽

Cited By ~ 2

Author(s):

D. R. Harkness ◽

L. Villa ◽

I. Berman ◽

J. B. Wilson ◽

T. H. J. Huisman

Keyword(s):

Type I ◽

Structural Studies ◽

Congenital Dyserythropoietic Anemia

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Structural studies on the [But-Cys18](19-37)-fragment of human β-calcitonin-gene-related peptide

Biochemical Journal ◽

10.1042/bj2800147 ◽

1991 ◽

Vol 280 (1) ◽

pp. 147-150 ◽

Cited By ~ 6

Author(s):

J K Sagoo ◽

C Bose ◽

N R A Beeley ◽

S J B Tendler

Keyword(s):

Calcitonin Gene Related Peptide ◽

Type I ◽

Immune Recognition ◽

Structural Studies ◽

Structural Elements ◽

Peptide Fragment ◽

Beta Turn ◽

Related Peptide ◽

Calcitonin Gene

High-field n.m.r. studies were undertaken upon a peptide fragment of the C-terminal region of human beta-calcitonin-gene-related peptide (beta-hCGRP). Studies on the antigenic [Bu(t)-Cys18]beta-hCGRP-(19-37)-fragment revealed that several elements of secondary structure were present when the peptide was dissolved in [2H6]dimethyl sulphoxide. In particular an unspecified turn in the region of Ser19-Gly20 and a type I beta-turn in the region of Asn31-Val32-Gly33 were identified. Through-space connections between the terminal Phe37 amide group and the beta-protons of Thr50 suggest that the peptide may be folded into a loop-type conformation. These structural elements appear to overlap with the epitopes of a number of monoclonal antibodies and provide a molecular basis for understanding the role of the terminal Phe37 amide residue in the immune recognition of beta-hCGRP.

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Synthesis and Use of DNA Containing a 5'-Bridging Phosphorothioate as a Suicide Substrate for Type I DNA Topoisomerases

DNA Topoisomerase Protocols ◽

10.1385/1-59259-057-8:119 ◽

2003 ◽

pp. 119-128

Author(s):

Alex B. Burgin

Keyword(s):

Type I ◽

Dna Topoisomerases ◽

Suicide Substrate

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An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1416485112 ◽

2015 ◽

Vol 112 (7) ◽

pp. E747-E756 ◽

Cited By ~ 110

Author(s):

TuAnh Ngoc Huynh ◽

Shukun Luo ◽

Daniel Pensinger ◽

John-Demian Sauer ◽

Liang Tong ◽

...

Keyword(s):

Practical Interest ◽

Stringent Response ◽

Adenosine Monophosphate ◽

Molecular Target ◽

Type I ◽

Structural Studies ◽

Chemical Proteomics ◽

Bacterial Signaling ◽

Hydrolysis Of ◽

Hydrolysis Activity

The nucleotide cyclic di-3′,5′- adenosine monophosphate (c-di-AMP) was recently identified as an essential and widespread second messenger in bacterial signaling. Among c-di-AMP–producing bacteria, altered nucleotide levels result in several physiological defects and attenuated virulence. Thus, a detailed molecular understanding of c-di-AMP metabolism is of both fundamental and practical interest. Currently, c-di-AMP degradation is recognized solely among DHH-DHHA1 domain-containing phosphodiesterases. Using chemical proteomics, we identified the Listeria monocytogenes protein PgpH as a molecular target of c-di-AMP. Biochemical and structural studies revealed that the PgpH His-Asp (HD) domain bound c-di-AMP with high affinity and specifically hydrolyzed this nucleotide to 5′-pApA. PgpH hydrolysis activity was inhibited by ppGpp, indicating a cross-talk between c-di-AMP signaling and the stringent response. Genetic analyses supported coordinated regulation of c-di-AMP levels in and out of the host. Intriguingly, a L. monocytogenes mutant that lacks c-di-AMP phosphodiesterases exhibited elevated c-di-AMP levels, hyperinduced a host type-I IFN response, and was significantly attenuated for infection. Furthermore, PgpH homologs, which belong to the 7TMR-HD family, are widespread among hundreds of c-di-AMP synthesizing microorganisms. Thus, PgpH represents a broadly conserved class of c-di-AMP phosphodiesterase with possibly other physiological functions in this crucial signaling network.

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