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- The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding
- Kim-Hung Huynh , Myoung-ki Hong , Clarice Lee , Huyen-Thi Tran , Sang Hee Lee , Yeh-Jin Ahn , Sun-Shin Cha , Lin-Woo Kang
- J. Microbiol. 2015;53(11):776-782. Published online October 28, 2015
- DOI: https://doi.org/10.1007/s12275-015-5475-8
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Abstract
- Acinetobacter baumannii, which is emerging as a multidrugresistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.
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Citations
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- In Silico Design and In Vitro Assessment of Bicyclic Trifluoromethylated Pyrroles as New Antibacterial and Antifungal Agents
Diana Hodyna, Anton Klipkov, Maryna Kachaeva, Yurii Shulha, Igor Gerus, Larysa Metelytsia, Vasyl Kovalishyn
Chemistry & Biodiversity.2024;[Epub] CrossRef - Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model
Jinxin Zhao, Yan Zhu, Jiru Han, Yu-Wei Lin, Michael Aichem, Jiping Wang, Ke Chen, Tony Velkov, Falk Schreiber, Jian Li
Microorganisms.2020; 8(11): 1793. CrossRef - Identification of natural inhibitors against Acinetobacter baumannii d-alanine-d-alanine ligase enzyme: A multi-spectrum in silico approach
Sajjad Ahmad, Saad Raza, Sumra Wajid Abbasi, Syed Sikander Azam
Journal of Molecular Liquids.2018; 262: 460. CrossRef - Molecular characterization of SCO0765 as a cellotriose releasing endo-β-1,4-cellulase from Streptomyces coelicolor A(3)
Joo-Bin Hong, Vijayalakshmi Dhakshnamoorthy, Chang-Ro Lee
Journal of Microbiology.2016; 54(9): 626. CrossRef
- In Silico Design and In Vitro Assessment of Bicyclic Trifluoromethylated Pyrroles as New Antibacterial and Antifungal Agents
- Crystal Structure of XoLAP, a Leucine Aminopeptidase, from Xanthomonas oryzae pv. oryzae
- Jin-Kwang Kim , Sampath Natarajan , Hanseul Park , Kim-Hung Huynh , Sang Hee Lee , Jeong-Gu Kim , Yeh-Jin Ahn , Lin-Woo Kang
- J. Microbiol. 2013;51(5):627-632. Published online October 31, 2013
- DOI: https://doi.org/10.1007/s12275-013-3234-2
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- 0 Download
- 7 Crossref
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Abstract
- Aminopeptidases are metalloproteinases that degrade N-terminal residues from protein and play important roles in cell growth and development by controlling cell homeostasis and protein maturation. We determined the crystal structure of XoLAP, a leucyl aminopeptidase, at 2.6 Å resolution from Xanthomonas oryzae pv. oryzae, causing the destructive rice disease of bacterial blight. It is the first crystal structure of aminopeptidase from phytopathogens as a drug target. XoLAP existed as a hexamer and the monomer structure consisted of an N-terminal cap domain and a C-terminal peptidase domain with two divalent zinc ions. XoLAP structure was compared with BlLAP and EcLAP (EcPepA) structures. Based on the structural comparison, the molecular model of XoLAP in complex with the natural aminopeptidase inhibitor of microginin FR1 was proposed. The model structure will be useful to develop a novel antibacterial drug against Xoo.
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Citations
Citations to this article as recorded by- Expression, Characterisation, Homology Modelling and Molecular Docking of a Novel M17 Family Leucyl-Aminopeptidase from Bacillus cereus CZ
Jie Liu, Tangbing Cui
International Journal of Molecular Sciences.2023; 24(21): 15939. CrossRef - Screening and verification for proteins that interact with leucine aminopeptidase of Taenia pisiformis using a yeast two-hybrid system
Shaohua Zhang
Parasitology Research.2019; 118(12): 3387. CrossRef - Transcriptional expression of aminoacyl tRNA synthetase genes of Xanthomonas oryzae pv. oryzae (Xoo) on rice-leaf extract treatment and crystal structure of Xoo glutamyl-tRNA synthetase
Thien-Hoang Ho, Myoung-Ki Hong, Seunghwan Kim, Jeong-Gu Kim, Jongha Lee, Kyoungho Jung, Inho Lee, Munyoung Choi, Hyunjae Park, Sanghee Lee, Yeh-Jin Ahn, Lin-Woo Kang
Crop and Pasture Science.2017; 68(5): 434. CrossRef - An angiotensin-converting enzyme-inhibitory metabolite with partial structure of microginin in a cyanobacterium Anabaena fertilissima CCC597, producing fibrinolytic protease
Suvendra Nath Bagchi, Shobha Sondhia, Manish Kumar Agrawal, Sonali Banerjee
Journal of Applied Phycology.2016; 28(1): 177. CrossRef - Structure and Substrate Recognition of the Bottromycin Maturation Enzyme BotP
Greg Mann, Liujie Huo, Sebastian Adam, Brunello Nardone, Jeremie Vendome, Nicholas James Westwood, Rolf Müller, Jesko Koehnke
ChemBioChem.2016; 17(23): 2286. CrossRef - Crystal Structures of Peptide Deformylase from Rice Pathogen Xanthomonas oryzae pv. oryzae in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds
Ho-Phuong-Thuy Ngo, Thien-Hoang Ho, Inho Lee, Huyen-Thi Tran, Bookyo Sur, Seunghwan Kim, Jeong-Gu Kim, Yeh-Jin Ahn, Sun-Shin Cha, Lin-Woo Kang
Journal of Agricultural and Food Chemistry.2016; 64(39): 7307. CrossRef - Crystallization and preliminary X-ray crystallographic analysis of the XoGroEL chaperonin fromXanthomonas oryzaepv.oryzae
Huyen-Thi Tran, Tan-Viet Pham, Ho-Phuong-Thuy Ngo, Myoung-Ki Hong, Jeong-Gu Kim, Sang Hee Lee, Yeh-Jin Ahn, Lin-Woo Kang
Acta Crystallographica Section F Structural Biology Communications.2014; 70(5): 604. CrossRef
- Expression, Characterisation, Homology Modelling and Molecular Docking of a Novel M17 Family Leucyl-Aminopeptidase from Bacillus cereus CZ
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