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Structure of New Delhi metallo-β-lactamase 1 (NDM-1).

Green VL, Verma A, Owens RJ, Phillips SE, Carr SB
Acta Crystallogr Sect F Struct Biol Cryst Commun 67 1160-4 (2011)
Cited: 43 times
EuropePMC logo PMID: 22102018

Abstract

Antibiotic resistance in bacterial pathogens poses a serious threat to human health and the metallo-β-lactamase (MBL) enzymes are responsible for much of this resistance. The recently identified New Delhi MBL 1 (NDM-1) is a novel member of this family that is capable of hydrolysing a wide variety of clinically important antibiotics. Here, the crystal structure of NDM-1 from Klebsiella pneumoniae is reported and its structure and active site are discussed in the context of other recently deposited coordinates of NDM-1.

Reviews - 3zr9 mentioned but not cited (1)

  1. The Continuing Challenge of Metallo-β-Lactamase Inhibition: Mechanism Matters. Ju LC, Cheng Z, Fast W, Bonomo RA, Crowder MW. Trends Pharmacol Sci 39 635-647 (2018)

Articles - 3zr9 mentioned but not cited (7)

  1. Structure of New Delhi metallo-β-lactamase 1 (NDM-1). Green VL, Verma A, Owens RJ, Phillips SE, Carr SB. Acta Crystallogr Sect F Struct Biol Cryst Commun 67 1160-1164 (2011)
  2. Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1. Zhang H, Ma G, Zhu Y, Zeng L, Ahmad A, Wang C, Pang B, Fang H, Zhao L, Hao Q. Antimicrob Agents Chemother 62 e01579-18 (2018)
  3. Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, Strynadka NCJ, Baker D. Proc Natl Acad Sci U S A 118 e2012800118 (2021)
  4. Investigating the position of the hairpin loop in New Delhi metallo-β-lactamase, NDM-1, during catalysis and inhibitor binding. Aitha M, Moller AJ, Sahu ID, Horitani M, Tierney DL, Crowder MW. J Inorg Biochem 156 35-39 (2016)
  5. A case study comparing quantitative stability-flexibility relationships across five metallo-β-lactamases highlighting differences within NDM-1. Brown MC, Verma D, Russell C, Jacobs DJ, Livesay DR. Methods Mol Biol 1084 227-238 (2014)
  6. Discovery of the Novel Inhibitor Against New Delhi Metallo-β-Lactamase Based on Virtual Screening and Molecular Modelling. Wang X, Yang Y, Gao Y, Niu X. Int J Mol Sci 21 E3567 (2020)
  7. Structural and biochemical characterization of the environmental MBLs MYO-1, ECV-1 and SHD-1. Fröhlich C, Sørum V, Huber S, Samuelsen Ø, Berglund F, Kristiansson E, Kotsakis SD, Marathe NP, Larsson DGJ, Leiros HS. J Antimicrob Chemother 75 2554-2563 (2020)


Reviews citing this publication (6)

  1. Resistance to antibiotics targeted to the bacterial cell wall. Nikolaidis I, Favini-Stabile S, Dessen A. Protein Sci 23 243-259 (2014)
  2. Metallo-ß-lactamases: a review. Behzadi P, García-Perdomo HA, Karpiński TM, Issakhanian L. Mol Biol Rep 47 6281-6294 (2020)
  3. Cadmium-zinc exchange and their binary relationship in the structure of Zn-related proteins: a mini review. Tang L, Qiu R, Tang Y, Wang S. Metallomics 6 1313-1323 (2014)
  4. Structural and functional insight of New Delhi Metallo β-lactamase-1 variants. Khan S, Ali A, Khan AU. Future Med Chem 10 221-229 (2018)
  5. A Systematic Review of the Effects of Satureja Khuzestanica Jamzad and Zataria Multiflora Boiss against Pseudomonas Aeruginosa. Khaledi A, Meskini M. Iran J Med Sci 45 83-90 (2020)
  6. Enzyme Inhibitors: The Best Strategy to Tackle Superbug NDM-1 and Its Variants. Li X, Zhao D, Li W, Sun J, Zhang X. Int J Mol Sci 23 197 (2021)

Articles citing this publication (29)

  1. Assay platform for clinically relevant metallo-β-lactamases. van Berkel SS, Brem J, Rydzik AM, Salimraj R, Cain R, Verma A, Owens RJ, Fishwick CW, Spencer J, Schofield CJ. J Med Chem 56 6945-6953 (2013)
  2. NDM-8 metallo-β-lactamase in a multidrug-resistant Escherichia coli strain isolated in Nepal. Tada T, Miyoshi-Akiyama T, Dahal RK, Sah MK, Ohara H, Kirikae T, Pokhrel BM. Antimicrob Agents Chemother 57 2394-2396 (2013)
  3. A novel New Delhi metallo-β-lactamase variant, NDM-14, isolated in a Chinese Hospital possesses increased enzymatic activity against carbapenems. Zou D, Huang Y, Zhao X, Liu W, Dong D, Li H, Wang X, Huang S, Wei X, Yan X, Yang Z, Tong Y, Huang L, Yuan J. Antimicrob Agents Chemother 59 2450-2453 (2015)
  4. Biochemical characterization of New Delhi metallo-β-lactamase variants reveals differences in protein stability. Makena A, Brem J, Pfeffer I, Geffen RE, Wilkins SE, Tarhonskaya H, Flashman E, Phee LM, Wareham DW, Schofield CJ. J Antimicrob Chemother 70 463-469 (2015)
  5. Plasmid-Mediated Novel blaNDM-17 Gene Encoding a Carbapenemase with Enhanced Activity in a Sequence Type 48 Escherichia coli Strain. Liu Z, Wang Y, Walsh TR, Liu D, Shen Z, Zhang R, Yin W, Yao H, Li J, Shen J. Antimicrob Agents Chemother 61 e02233-16 (2017)
  6. Diaryl-substituted azolylthioacetamides: Inhibitor discovery of New Delhi metallo-β-lactamase-1 (NDM-1). Zhang YL, Yang KW, Zhou YJ, LaCuran AE, Oelschlaeger P, Crowder MW. ChemMedChem 9 2445-2448 (2014)
  7. Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling. Chen J, Wang J, Zhu W. Phys Chem Chem Phys 19 3067-3075 (2017)
  8. Novel Variant of New Delhi Metallo-β-lactamase, NDM-20, in Escherichia coli. Liu Z, Li J, Wang X, Liu D, Ke Y, Wang Y, Shen J. Front Microbiol 9 248 (2018)
  9. NDM-12, a novel New Delhi metallo-β-lactamase variant from a carbapenem-resistant Escherichia coli clinical isolate in Nepal. Tada T, Shrestha B, Miyoshi-Akiyama T, Shimada K, Ohara H, Kirikae T, Pokhrel BM. Antimicrob Agents Chemother 58 6302-6305 (2014)
  10. Search of potential inhibitor against New Delhi metallo-beta-lactamase 1 from a series of antibacterial natural compounds. Thakur PK, Kumar J, Ray D, Anjum F, Hassan MI. J Nat Sci Biol Med 4 51-56 (2013)
  11. Biochemical analysis of metallo-β-lactamase NDM-3 from a multidrug-resistant Escherichia coli strain isolated in Japan. Tada T, Miyoshi-Akiyama T, Shimada K, Kirikae T. Antimicrob Agents Chemother 58 3538-3540 (2014)
  12. A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1. Zhu K, Lu J, Liang Z, Kong X, Ye F, Jin L, Geng H, Chen Y, Zheng M, Jiang H, Li JQ, Luo C. J Comput Aided Mol Des 27 247-256 (2013)
  13. Role of Non-Active-Site Residue Trp-93 in the Function and Stability of New Delhi Metallo-β-Lactamase 1. Khan AU, Rehman MT. Antimicrob Agents Chemother 60 356-360 (2016)
  14. Covalent inhibition of New Delhi metallo-β-lactamase-1 (NDM-1) by cefaclor. Thomas PW, Cammarata M, Brodbelt JS, Fast W. Chembiochem 15 2541-2548 (2014)
  15. Pterostilbene restores carbapenem susceptibility in New Delhi metallo-β-lactamase-producing isolates by inhibiting the activity of New Delhi metallo-β-lactamases. Liu S, Zhang J, Zhou Y, Hu N, Li J, Wang Y, Niu X, Deng X, Wang J. Br J Pharmacol 176 4548-4557 (2019)
  16. The Reaction Mechanism of Metallo-β-Lactamases Is Tuned by the Conformation of an Active-Site Mobile Loop. Palacios AR, Mojica MF, Giannini E, Taracila MA, Bethel CR, Alzari PM, Otero LH, Klinke S, Llarrull LI, Bonomo RA, Vila AJ. Antimicrob Agents Chemother 63 e01754-18 (2019)
  17. Chromophore-linked substrate (CLS405): probing metallo-β-lactamase activity and inhibition. Makena A, van Berkel SS, Lejeune C, Owens RJ, Verma A, Salimraj R, Spencer J, Brem J, Schofield CJ. ChemMedChem 8 1923-1929 (2013)
  18. Emergence of Hybrid Resistance and Virulence Plasmids Harboring New Delhi Metallo-β-Lactamase in Klebsiella pneumoniae in Russia. Starkova P, Lazareva I, Avdeeva A, Sulian O, Likholetova D, Ageevets V, Lebedeva M, Gostev V, Sopova J, Sidorenko S. Antibiotics (Basel) 10 691 (2021)
  19. An evolutionarily conserved allosteric site modulates beta-lactamase activity. Avci FG, Altinisik FE, Vardar Ulu D, Ozkirimli Olmez E, Sariyar Akbulut B. J Enzyme Inhib Med Chem 31 33-40 (2016)
  20. Mechanistic Investigations of Metallo-β-lactamase Inhibitors: Strong Zinc Binding Is Not Required for Potent Enzyme Inhibition*. Wade N, Tehrani KHME, Brüchle NC, van Haren MJ, Mashayekhi V, Martin NI. ChemMedChem 16 1651-1659 (2021)
  21. Discovery of novel new Delhi metallo-β-lactamases-1 inhibitors by multistep virtual screening. Wang X, Lu M, Shi Y, Ou Y, Cheng X. PLoS One 10 e0118290 (2015)
  22. NMR Characterization of the Influence of Zinc(II) Ions on the Structural and Dynamic Behavior of the New Delhi Metallo-β-Lactamase-1 and on the Binding with Flavonols as Inhibitors. Rivière G, Oueslati S, Gayral M, Créchet JB, Nhiri N, Jacquet E, Cintrat JC, Giraud F, van Heijenoort C, Lescop E, Pethe S, Iorga BI, Naas T, Guittet E, Morellet N. ACS Omega 5 10466-10480 (2020)
  23. Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo-β-lactamase 1. Prunotto A, Bahr G, González LJ, Vila AJ, Dal Peraro M. ACS Infect Dis 6 2719-2731 (2020)
  24. Molecular Characterization and Computational Modelling of New Delhi Metallo-β-Lactamase-5 from an Escherichia coli Isolate (KOEC3) of Bovine Origin. Purkait D, Ahuja A, Bhattacharjee U, Singha A, Rhetso K, Dey TK, Das S, Sanjukta RK, Puro K, Shakuntala I, Sen A, Banerjee A, Sharma I, Bhatta RS, Mawlong M, Guha C, Pradhan NR, Ghatak S. Indian J Microbiol 56 182-189 (2016)
  25. Association between Presence of RmpA, MrkA and MrkD Genes and Antibiotic Resistance in Clinical Klebsiella pneumoniae Isolates from Hospitals in Tehran, Iran. Bakhtiari R, Javadi A, Aminzadeh M, Molaee-Aghaee E, Shaffaghat Z. Iran J Public Health 50 1009-1016 (2021)
  26. Exploring the Role of L10 Loop in New Delhi Metallo-β-lactamase (NDM-1): Kinetic and Dynamic Studies. Piccirilli A, Criscuolo E, Brisdelli F, Mercuri PS, Cherubini S, De Sciscio ML, Maccarrone M, Galleni M, Amicosante G, Perilli M. Molecules 26 5489 (2021)
  27. Mechanism of imipenem resistance in metallo-β-lactamases expressing pathogenic bacterial spp. and identification of potential inhibitors: An in silico approach. Malathi K, Ramaiah S. J Cell Biochem 120 584-591 (2019)
  28. Prediction of Phytochemicals for Their Potential to Inhibit New Delhi Metallo β-Lactamase (NDM-1). Bibi Z, Asghar I, Ashraf NM, Zeb I, Rashid U, Hamid A, Ali MK, Hatamleh AA, Al-Dosary MA, Ahmad R, Ali M. Pharmaceuticals (Basel) 16 1404 (2023)
  29. Preparation and evaluation of the exotoxin A nano-gold conjugate as a vaccine candidate for Pseudomonas aeruginosa infections. Abbasi M, Tanomand A, Kafilzadeh F, Zolghadri S, Hosainzadegan H. Iran J Basic Med Sci 24 1366-1372 (2021)


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