Structure, Assembly, and Mechanism of a PLP-Dependent Dodecameric l-Aspartate β-Decarboxylase

Hui Ju Chen; Tzu Ping Ko; Chia Yin Lee; Nai Chen Wang; Andrew H.J. Wang

doi:10.1016/j.str.2009.02.013

Structure, Assembly, and Mechanism of a PLP-Dependent Dodecameric l-Aspartate β-Decarboxylase

Hui Ju Chen, Tzu Ping Ko, Chia Yin Lee, Nai Chen Wang, Andrew H.J. Wang

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

25 Citations (Scopus)

Abstract

The type-I PLP enzyme l-aspartate β-decarboxylase converts aspartate to alanine and CO₂. Similar to the homodimeric aminotransferases, its protein subunit comprises a large and a small domain, of 410 and 120 residues, respectively. The crystal structure reveals a dodecamer made of six identical dimers arranged in a truncated tetrahedron whose assembly involves tetramer and hexamer as intermediates. The additional helical motifs I and II participate in the oligomer formation. Triple mutations of S67R/Y68R/M69R or S67E/Y68E/M69E in motif I produced an inactive dimer. The PLP is bound covalently to Lys315 in the active site, while its phosphate group interacts with a neighboring Tyr134. Removal of the bulky side chain of Arg37, which overhangs the PLP group, improved the substrate affinity. Mutations in flexible regions produced the more active K17A and the completely inactive R487A. The structure also suggests that substrate binding triggers conformational changes essential for catalyzing the reaction.

Original language	English
Pages (from-to)	517-529
Number of pages	13
Journal	Structure
Volume	17
Issue number	4
DOIs	https://doi.org/10.1016/j.str.2009.02.013
Publication status	Published - Apr 15 2009
Externally published	Yes

Keywords

PROTEINS

ASJC Scopus subject areas

Structural Biology
Molecular Biology

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10.1016/j.str.2009.02.013

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title = "Structure, Assembly, and Mechanism of a PLP-Dependent Dodecameric l-Aspartate β-Decarboxylase",

abstract = "The type-I PLP enzyme l-aspartate β-decarboxylase converts aspartate to alanine and CO2. Similar to the homodimeric aminotransferases, its protein subunit comprises a large and a small domain, of 410 and 120 residues, respectively. The crystal structure reveals a dodecamer made of six identical dimers arranged in a truncated tetrahedron whose assembly involves tetramer and hexamer as intermediates. The additional helical motifs I and II participate in the oligomer formation. Triple mutations of S67R/Y68R/M69R or S67E/Y68E/M69E in motif I produced an inactive dimer. The PLP is bound covalently to Lys315 in the active site, while its phosphate group interacts with a neighboring Tyr134. Removal of the bulky side chain of Arg37, which overhangs the PLP group, improved the substrate affinity. Mutations in flexible regions produced the more active K17A and the completely inactive R487A. The structure also suggests that substrate binding triggers conformational changes essential for catalyzing the reaction.",

keywords = "PROTEINS",

author = "Chen, {Hui Ju} and Ko, {Tzu Ping} and Lee, {Chia Yin} and Wang, {Nai Chen} and Wang, {Andrew H.J.}",

note = "Funding Information: We thank National Synchrotron Radiation Research Center of Taiwan, Photon Factory of Japan, and Advanced Light Source of UC Berkeley for beam time allocations. We also thank Shu-Chuan Jao and Hui-Chuan Chang for their advice in the ITC and AUC experiments. This work was supported by grants from the National Science Council of Taiwan, ROC (NSC94-2313-B-002-049 and NSC95-2811-B-002-055 to C.Y.L. and NSC-95-3112-B-011-015-Y to A.H.J.W.). ",

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AU - Chen, Hui Ju

AU - Ko, Tzu Ping

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AU - Wang, Nai Chen

AU - Wang, Andrew H.J.

N1 - Funding Information: We thank National Synchrotron Radiation Research Center of Taiwan, Photon Factory of Japan, and Advanced Light Source of UC Berkeley for beam time allocations. We also thank Shu-Chuan Jao and Hui-Chuan Chang for their advice in the ITC and AUC experiments. This work was supported by grants from the National Science Council of Taiwan, ROC (NSC94-2313-B-002-049 and NSC95-2811-B-002-055 to C.Y.L. and NSC-95-3112-B-011-015-Y to A.H.J.W.).

PY - 2009/4/15

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N2 - The type-I PLP enzyme l-aspartate β-decarboxylase converts aspartate to alanine and CO2. Similar to the homodimeric aminotransferases, its protein subunit comprises a large and a small domain, of 410 and 120 residues, respectively. The crystal structure reveals a dodecamer made of six identical dimers arranged in a truncated tetrahedron whose assembly involves tetramer and hexamer as intermediates. The additional helical motifs I and II participate in the oligomer formation. Triple mutations of S67R/Y68R/M69R or S67E/Y68E/M69E in motif I produced an inactive dimer. The PLP is bound covalently to Lys315 in the active site, while its phosphate group interacts with a neighboring Tyr134. Removal of the bulky side chain of Arg37, which overhangs the PLP group, improved the substrate affinity. Mutations in flexible regions produced the more active K17A and the completely inactive R487A. The structure also suggests that substrate binding triggers conformational changes essential for catalyzing the reaction.

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Structure, Assembly, and Mechanism of a PLP-Dependent Dodecameric l-Aspartate β-Decarboxylase

Abstract

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