Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants
The increasing incidence of community- and hospital-acquired infections with multidrug-resistant (MDR) bacteria poses a critical threat to public health and the healthcare system. Although β-lactam antibiotics are effective against most bacterial infections, some bacteria are resistant to β-lactam a...
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MDPI AG
2020-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/14/4926 |
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| author | Yoon Sik Park Tae Yeong Kim Hyunjae Park Jung Hun Lee Diem Quynh Nguyen Myoung-Ki Hong Sang Hee Lee Lin-Woo Kang |
| author_facet | Yoon Sik Park Tae Yeong Kim Hyunjae Park Jung Hun Lee Diem Quynh Nguyen Myoung-Ki Hong Sang Hee Lee Lin-Woo Kang |
| author_sort | Yoon Sik Park |
| collection | DOAJ |
| description | The increasing incidence of community- and hospital-acquired infections with multidrug-resistant (MDR) bacteria poses a critical threat to public health and the healthcare system. Although β-lactam antibiotics are effective against most bacterial infections, some bacteria are resistant to β-lactam antibiotics by producing β-lactamases. Among β-lactamases, metallo-β-lactamases (MBLs) are especially worrisome as only a few inhibitors have been developed against them. In MBLs, the metal ions play an important role as they coordinate a catalytic water molecule that hydrolyzes β-lactam rings. We determined the crystal structures of different variants of PNGM-1, an ancient MBL with additional tRNase Z activity. The variants were generated by site-directed mutagenesis targeting metal-coordinating residues. In PNGM-1, both zinc ions are coordinated by six coordination partners in an octahedral geometry, and the zinc-centered octahedrons share a common face. Structures of the PNGM-1 variants confirm that the substitution of a metal-coordinating residue causes the loss of metal binding and β-lactamase activity. Compared with PNGM-1, subclass B3 MBLs lack one metal-coordinating residue, leading to a shift in the metal-coordination geometry from an octahedral to tetrahedral geometry. Our results imply that a subtle change in the metal-binding site of MBLs can markedly change their metal-coordination geometry and catalytic activity. |
| first_indexed | 2024-03-10T18:31:48Z |
| format | Article |
| id | doaj.art-a29c7bbc2c6e43fb8392c6945d0c0f65 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T18:31:48Z |
| publishDate | 2020-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-a29c7bbc2c6e43fb8392c6945d0c0f652023-11-20T06:34:35ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-07-012114492610.3390/ijms21144926Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 VariantsYoon Sik Park0Tae Yeong Kim1Hyunjae Park2Jung Hun Lee3Diem Quynh Nguyen4Myoung-Ki Hong5Sang Hee Lee6Lin-Woo Kang7Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, KoreaNational Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, KoreaDepartment of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, KoreaNational Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, KoreaDepartment of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, KoreaDepartment of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, KoreaNational Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, KoreaDepartment of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, KoreaThe increasing incidence of community- and hospital-acquired infections with multidrug-resistant (MDR) bacteria poses a critical threat to public health and the healthcare system. Although β-lactam antibiotics are effective against most bacterial infections, some bacteria are resistant to β-lactam antibiotics by producing β-lactamases. Among β-lactamases, metallo-β-lactamases (MBLs) are especially worrisome as only a few inhibitors have been developed against them. In MBLs, the metal ions play an important role as they coordinate a catalytic water molecule that hydrolyzes β-lactam rings. We determined the crystal structures of different variants of PNGM-1, an ancient MBL with additional tRNase Z activity. The variants were generated by site-directed mutagenesis targeting metal-coordinating residues. In PNGM-1, both zinc ions are coordinated by six coordination partners in an octahedral geometry, and the zinc-centered octahedrons share a common face. Structures of the PNGM-1 variants confirm that the substitution of a metal-coordinating residue causes the loss of metal binding and β-lactamase activity. Compared with PNGM-1, subclass B3 MBLs lack one metal-coordinating residue, leading to a shift in the metal-coordination geometry from an octahedral to tetrahedral geometry. Our results imply that a subtle change in the metal-binding site of MBLs can markedly change their metal-coordination geometry and catalytic activity.https://www.mdpi.com/1422-0067/21/14/4926metallo-β-lactamase (MBL)metal coordinationantibioticsx-ray crystallography |
| spellingShingle | Yoon Sik Park Tae Yeong Kim Hyunjae Park Jung Hun Lee Diem Quynh Nguyen Myoung-Ki Hong Sang Hee Lee Lin-Woo Kang Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants International Journal of Molecular Sciences metallo-β-lactamase (MBL) metal coordination antibiotics x-ray crystallography |
| title | Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants |
| title_full | Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants |
| title_fullStr | Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants |
| title_full_unstemmed | Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants |
| title_short | Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants |
| title_sort | structural study of metal binding and coordination in ancient metallo β lactamase pngm 1 variants |
| topic | metallo-β-lactamase (MBL) metal coordination antibiotics x-ray crystallography |
| url | https://www.mdpi.com/1422-0067/21/14/4926 |
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