Evidence map›Paper›PMID 40891210›Full record

ArticleBioscience reports2025

Kinetic and homology model analysis of diaminopimelate decarboxylase from Cyanothece sp. ATCC 51142: unveiling a key enzyme in lysine biosynthesis.

Zhi-Min Li, Suhang Chen, Weikang Luo, Fang Wang, Siqi Wang, Liyang Huang, Xinyue Xiong, Congcong Xie, Zhimin Li

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Article in Bioscience reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

9 authors.

Zhi-Min LiCollege of Chemistry and Materials, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.
Suhang ChenCollege of Bioscience and Bioengineering, Jiangxi Provincial Key Laboratory for Postharvest Storage and Preservation of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.
Weikang LuoCollege of Bioscience and Bioengineering, Jiangxi Provincial Key Laboratory for Postharvest Storage and Preservation of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.
Fang WangJiangxi Provincial Psychiatric Hospital, Nanchang, Jiangxi, 330000, China.
Siqi WangCollege of Bioscience and Bioengineering, Jiangxi Provincial Key Laboratory for Postharvest Storage and Preservation of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.
Liyang HuangCollege of Bioscience and Bioengineering, Jiangxi Provincial Key Laboratory for Postharvest Storage and Preservation of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.
Xinyue XiongCollege of Bioscience and Bioengineering, Jiangxi Provincial Key Laboratory for Postharvest Storage and Preservation of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.
Congcong XieSchool of Biological and Environmental Engineering, Jingdezhen University, Jingdezhen, Jiangxi, 333000, China.
Zhimin LiCollege of Chemistry and Materials, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.ORCID 0000-0001-7036-9282

Funding

Natural Science Foundation of China 32160219
6 · The paper itself

Abstract

Diaminopimelate decarboxylase (DAPDC), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, catalyzes the decarboxylation of diaminopimelate (DAP) to yield L-lysine, a key step in lysine biosynthesis. This present study presents a preliminary characterization of DAPDC encoded by the cce1351 gene in Cyanothece sp. ATCC 51142 (CsDAPDC), focusing on its biochemical properties and model structure characteristics. The enzyme exhibited a peak activity at 30°C and pH 8.0, and the catalytic constant (kcat) and substrate binding affinity Michaelis constant (KM) were determined as 1.68 s-1 and 1.20 mM at the above-mentioned condition, respectively. Homology modeling and molecular docking analysis revealed that Gly286, Gly330, Tyr428, and Asp118 interacted with the PLP cofactor, and Ser249, Tyr372, and Tyr428 interacted with the DAP substrate. Additionally, Cys399, Glu400, and Tyr436 from the other monomer were also involved in binding DAP and PLP. Site-directed mutagenesis confirmed the functional roles of these key residues in catalysis. This work provides valuable insights into the catalytic mechanism of CsDAPDC and highlights the enzyme's potential for applications in metabolic engineering of cyanobacteria for enhanced lysine production.

Indexed as

Bacterial ProteinsCarboxy-LyasesCyanotheceLysineDiaminopimelic AcidKineticsMolecular Docking SimulationMutagenesis, Site-DirectedPyridoxal PhosphateSubstrate SpecificityBacterial ProteinsCarboxy-LyasesDiaminopimelic Aciddiaminopimelic acid decarboxylaseLysinePyridoxal PhosphateCyanothece sp. ATCC 51142diaminopimelate decarboxylaseenzymatic kineticshomology modelinglysine biosynthesismolecular docking

Identifiers

PMID40891210
PMCPMC12599289

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