Crystal structure of ferric-yersiniabactin, a virulence factor of Yersinia pestis

M. Clarke Miller; Sean Parkin; Jacqueline D. Fetherston; Robert D. Perry; Edward DeMoll

doi:10.1016/j.jinorgbio.2006.04.007

Crystal structure of ferric-yersiniabactin, a virulence factor of Yersinia pestis

M. Clarke Miller, Sean Parkin, Jacqueline D. Fetherston, Robert D. Perry, Edward DeMoll

Chemistry

Research output: Contribution to journal › Article › peer-review

50 Scopus citations

Abstract

Yersiniabactin (Ybt), the siderophore produced by Yersinia pestis, has been crystallized successfully in the ferric complex form and the crystal structure has been determined. The crystals are orthorhombic with a space group of P2₁2₁2₁ and four distinct molecules per unit cell with cell dimensions of a = 11.3271(±0.0003) Å, b = 22.3556(±0.0006) Å, and c = 39.8991(±0.0011) Å. The crystal structure of ferric Ybt shows that the ferric ion is coordinated as a 1:1 complex by three nitrogen electron pairs and three negatively charged oxygen atoms with a distorted octahedral coordination. The molecule displays a Δ absolute configuration with chiral centers at N2, C9, C10, C12, C13, and C19 in R, R, R, R, S, S configurations, respectively. Few of the crystal structures of siderophores have been solved, and those which have been are of simple hydroxamate and catechol types such as ferrioxamine B and agrobactin. To our knowledge this is the first report of the ferric crystal structure of 5-member heterocycle siderophore.

Original language	English
Pages (from-to)	1495-1500
Number of pages	6
Journal	Journal of Inorganic Biochemistry
Volume	100
Issue number	9
DOIs	https://doi.org/10.1016/j.jinorgbio.2006.04.007
State	Published - Sep 2006

Bibliographical note

Funding Information:
This work was supported by Public Health Service grant AI33481 to ED, JDF, and RDP from the National Institutes of Health. We would also like to thank Mr. Jeff Withers for his insight and for technical discussions with him.

Funding

This work was supported by Public Health Service grant AI33481 to ED, JDF, and RDP from the National Institutes of Health. We would also like to thank Mr. Jeff Withers for his insight and for technical discussions with him.

Funders	Funder number
National Institutes of Health (NIH)
Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases	R56AI033481
Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases
U.S. Public Health Service

Keywords

Crystal
Siderophore
X-ray diffraction
Yersinia pestis
Yersiniabactin

ASJC Scopus subject areas

Biochemistry
Inorganic Chemistry

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10.1016/j.jinorgbio.2006.04.007

Cite this

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title = "Crystal structure of ferric-yersiniabactin, a virulence factor of Yersinia pestis",

abstract = "Yersiniabactin (Ybt), the siderophore produced by Yersinia pestis, has been crystallized successfully in the ferric complex form and the crystal structure has been determined. The crystals are orthorhombic with a space group of P212121 and four distinct molecules per unit cell with cell dimensions of a = 11.3271(±0.0003) {\AA}, b = 22.3556(±0.0006) {\AA}, and c = 39.8991(±0.0011) {\AA}. The crystal structure of ferric Ybt shows that the ferric ion is coordinated as a 1:1 complex by three nitrogen electron pairs and three negatively charged oxygen atoms with a distorted octahedral coordination. The molecule displays a Δ absolute configuration with chiral centers at N2, C9, C10, C12, C13, and C19 in R, R, R, R, S, S configurations, respectively. Few of the crystal structures of siderophores have been solved, and those which have been are of simple hydroxamate and catechol types such as ferrioxamine B and agrobactin. To our knowledge this is the first report of the ferric crystal structure of 5-member heterocycle siderophore.",

keywords = "Crystal, Siderophore, X-ray diffraction, Yersinia pestis, Yersiniabactin",

author = "Miller, \{M. Clarke\} and Sean Parkin and Fetherston, \{Jacqueline D.\} and Perry, \{Robert D.\} and Edward DeMoll",

note = "Funding Information: This work was supported by Public Health Service grant AI33481 to ED, JDF, and RDP from the National Institutes of Health. We would also like to thank Mr. Jeff Withers for his insight and for technical discussions with him. ",

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language = "English",

volume = "100",

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T1 - Crystal structure of ferric-yersiniabactin, a virulence factor of Yersinia pestis

AU - Miller, M. Clarke

AU - Parkin, Sean

AU - Fetherston, Jacqueline D.

AU - Perry, Robert D.

AU - DeMoll, Edward

N1 - Funding Information: This work was supported by Public Health Service grant AI33481 to ED, JDF, and RDP from the National Institutes of Health. We would also like to thank Mr. Jeff Withers for his insight and for technical discussions with him.

PY - 2006/9

Y1 - 2006/9

N2 - Yersiniabactin (Ybt), the siderophore produced by Yersinia pestis, has been crystallized successfully in the ferric complex form and the crystal structure has been determined. The crystals are orthorhombic with a space group of P212121 and four distinct molecules per unit cell with cell dimensions of a = 11.3271(±0.0003) Å, b = 22.3556(±0.0006) Å, and c = 39.8991(±0.0011) Å. The crystal structure of ferric Ybt shows that the ferric ion is coordinated as a 1:1 complex by three nitrogen electron pairs and three negatively charged oxygen atoms with a distorted octahedral coordination. The molecule displays a Δ absolute configuration with chiral centers at N2, C9, C10, C12, C13, and C19 in R, R, R, R, S, S configurations, respectively. Few of the crystal structures of siderophores have been solved, and those which have been are of simple hydroxamate and catechol types such as ferrioxamine B and agrobactin. To our knowledge this is the first report of the ferric crystal structure of 5-member heterocycle siderophore.

AB - Yersiniabactin (Ybt), the siderophore produced by Yersinia pestis, has been crystallized successfully in the ferric complex form and the crystal structure has been determined. The crystals are orthorhombic with a space group of P212121 and four distinct molecules per unit cell with cell dimensions of a = 11.3271(±0.0003) Å, b = 22.3556(±0.0006) Å, and c = 39.8991(±0.0011) Å. The crystal structure of ferric Ybt shows that the ferric ion is coordinated as a 1:1 complex by three nitrogen electron pairs and three negatively charged oxygen atoms with a distorted octahedral coordination. The molecule displays a Δ absolute configuration with chiral centers at N2, C9, C10, C12, C13, and C19 in R, R, R, R, S, S configurations, respectively. Few of the crystal structures of siderophores have been solved, and those which have been are of simple hydroxamate and catechol types such as ferrioxamine B and agrobactin. To our knowledge this is the first report of the ferric crystal structure of 5-member heterocycle siderophore.

KW - Crystal

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KW - X-ray diffraction

KW - Yersinia pestis

KW - Yersiniabactin

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Crystal structure of ferric-yersiniabactin, a virulence factor of Yersinia pestis

Abstract

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

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