High resolution crystal structure of the catalytic domain of MCR-1

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Ma, Guixing ^a   Zhu, Yifan ^a   Yu, Zhicheng ^a   Ahmad, Ashfaq ^a   Zhang, Hongmin ^a  

^a SOUTHERN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; CATION; COLISTIN; EPTC PROTEIN, E COLI; ESCHERICHIA COLI PROTEIN; ETHANOLAMINE DERIVATIVE; ION; LIPID A; LPTA PROTEIN, E COLI; MCR-1 PROTEIN, E COLI; MEMBRANE PROTEIN; PHOSPHOETHANOLAMINE; PROTEIN BINDING; WATER;

BINDING SITE; CHEMISTRY; ENZYME ACTIVE SITE; MOLECULAR MODEL; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CARRIER PROTEINS; CATALYTIC DOMAIN; CATIONS; COLISTIN; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI PROTEINS; ETHANOLAMINES; IONS; LIPID A; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; WATER;

EID: 85007014285     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep39540     Document Type: Article

References (62)

1. Boucher, H. W. et al. Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America. Clinical Infectious Diseases 48, 1-12, doi: 10.1086/595011 (2009).
2. Bonomo, R. A. & Szabo, D. Mechanisms of multidrug resistance in Acinetobacter species and Pseudomonas aeruginosa. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America 43 Suppl 2, S49-56, doi: 10.1086/504477 (2006).
3. Rahal, J. J. Novel antibiotic combinations against infections with almost completely resistant Pseudomonas aeruginosa and Acinetobacter species. Clinical Infectious Diseases 43, S95-S99, doi: 10.1086/504486 (2006).
4. Livermore, D. M. Has the era of untreatable infections arrived? J Antimicrob Chemoth 64, 29-36, doi: 10.1093/jac/dkp255 (2009).
5. Moellering, R. C. NDM-1 - A Cause for Worldwide Concern. New Engl J Med 363, 2377-2379, doi: 10.1056/NEJMp1011715 (2010).
6. Yigit, H. et al. Novel carbapenem-hydrolyzing beta-lactamase, KPC-1, from a carbapenem-resistant strain of Klebsiella pneumoniae. Antimicrob Agents Ch 45, 1151-1161 (2001).
7. Yong, D. et al. Characterization of a New Metallo-beta-Lactamase Gene, bla(NDM-1), and a Novel Erythromycin Esterase Gene Carried on a Unique Genetic Structure in Klebsiella pneumoniae Sequence Type 14 from India. Antimicrob Agents Ch 53, 5046-5054, doi: 10.1128/Aac.00774-09 (2009).
8. Baiden, F., Owusu-Agyei, S., Webster, J. & Chandramohan, D. The need for new antibiotics. Lancet 375, 637-638 (2010).
9. Struelens, M. J. et al. New Delhi metallo-beta-lactamase 1-producing Enterobacteriaceae: emergence and response in Europe. Eurosurveillance 15, 9-16 (2010).
10. Kumarasamy, K. K. et al. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect Dis 10, 597-602, doi: 10.1016/S1473-3099(10)70143-2 (2010).
11. Munoz-Price, L. S. et al. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect Dis 13, 785-796, doi: 10.1016/S1473-3099(13)70190-7 (2013).
12. Paterson, D. L. & Harris, P. N. A. Colistin resistance: a major breach in our last line of defence. Lancet Infect Dis 16, 132-133, doi: 10.1016/S1473-3099(15)00463-6 (2016).
13. Doyle, M. P., Loneragan, G. H., Scott, H. M. & Singer, R. S. Antimicrobial Resistance: Challenges and Perspectives. Comprehensive Reviews in Food Science and Food Safety 12, 234-248, doi: 10.1111/1541-4337.12008 (2013).
14. Liu, Y. Y. et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis 16, 161-168, doi: 10.1016/S1473-3099(15)00424-7 (2016).
15. Hasman, H. et al. Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015. Euro Surveill 20, doi: 10.2807/1560-7917.ES.2015.20.49.30085 (2015).
16. Falgenhauer, L. et al. Colistin resistance gene mcr-1 in extended-spectrum beta-lactamase-producing and carbapenemase-producing Gram-negative bacteria in Germany. Lancet Infect Dis, doi: 10.1016/S1473-3099(16)00009-8 (2016).
17. Perrin-Guyomard, A. et al. Prevalence of mcr-1 in commensal Escherichia coli from French livestock, 2007 to 2014. Euro Surveill 21, doi: 10.2807/1560-7917.ES.2016.21.6.30135 (2016).
18. Kluytmans-van den Bergh, M. F. et al. Presence of mcr-1-positive Enterobacteriaceae in retail chicken meat but not in humans in the Netherlands since 2009. Eurosurveillance 21, 12-18, doi: 10.2807/1560-7917.Es.2016.21.9.30149 (2016).
19. Zurfuh, K. et al. Occurrence of the plasmid-borne mcr-1 colistin resistance gene in ESBL-producing Enterobacteriacae in river water and imported vegetable samples in Switzerland. Antimicrob Agents Chemother, doi: 10.1128/AAC.00066-16 (2016).
20. McGann, P. et al. Escherichia coli Harboring mcr-1 and blaCTX-M on a Novel IncF Plasmid: First report of mcr-1 in the USA. Antimicrob Agents Chemother, doi: 10.1128/AAC.01103-16 (2016).
21. Malhotra-Kumar, S. et al. Colistin resistance gene mcr-1 harboured on a multidrug resistant plasmid. Lancet Infect Dis, doi: 10.1016/S1473-3099(16)00012-8 (2016).
22. Cannatelli, A. et al. First Detection of the mcr-1 Colistin Resistance Gene in Escherichia coli in Italy. Antimicrob Agents Chemother 60, 3257-3258, doi: 10.1128/AAC.00246-16 (2016).
23. Malhotra-Kumar, S. et al. Colistin-resistant Escherichia coli harbouring mcr-1 isolated from food animals in Hanoi, Vietnam. Lancet Infect Dis, doi: 10.1016/S1473-3099(16)00014-1 (2016).
24. Kempf, I. et al. What do we know about resistance to colistin in Enterobacteriaceae in avian and pig production in Europe? Int J Antimicrob Ag 42, 379-383 (2013).
25. Gunn, J. S. The Salmonella PmrAB regulon: lipopolysaccharide modifications, antimicrobial peptide resistance and more. Trends in microbiology 16, 284-290 (2008).
26. Cannatelli, A. et al. In Vivo Emergence of Colistin Resistance in Klebsiella pneumoniae Producing KPC-Type Carbapenemases Mediated by Insertional Inactivation of the PhoQ/PhoP mgrB Regulator. Antimicrob Agents Ch 57, 5521-5526 (2013).
27. Yao, X., Doi, Y., Zeng, L., Lv, L. & Liu, J. H. Carbapenem-resistant and colistin-resistant Escherichia coli co-producing NDM-9 and MCR-1. Lancet Infect Dis, doi: 10.1016/S1473-3099(16)00057-8 (2016).
28. Haenni, M. et al. Co-occurrence of extended spectrum beta lactamase and MCR-1 encoding genes on plasmids. Lancet Infect Dis, doi: 10.1016/S1473-3099(16)00007-4 (2016).
29. Yang, Y. Q. et al. Co-occurrence of mcr-1 and ESBL on a single plasmid in Salmonella enterica. The Journal of antimicrobial chemotherapy, doi: 10.1093/jac/dkw243 (2016).
30. Du, H., Chen, L., Tang, Y. W. & Kreiswirth, B. N. Emergence of the mcr-1 colistin resistance gene in carbapenem-resistant Enterobacteriaceae. Lancet Infect Dis, doi: 10.1016/S1473-3099(16)00056-6 (2016).
31. Di Pilato, V. et al. MCR-1.2: a new MCR variant encoded by a transferable plasmid from a colistin-resistant KPC carbapenemase-producing Klebsiella pneumoniae of sequence type 512. Antimicrob Agents Chemother, doi: 10.1128/AAC.01075-16 (2016).
32. Cox, A. D. et al. Phosphorylation of the lipid a region of meningococcal lipopolysaccharide: Identification of a family of transferases that add phosphoethanolamine to lipopolysaccharide. Journal of bacteriology 185, 3270-3277, doi: 10.1128/Jb.185.3270.3277.2003 (2003).
33. Wanty, C. et al. The Structure of the Neisserial Lipooligosaccharide Phosphoethanolamine Transferase A (LptA) Required for Resistance to Polymyxin. Journal of molecular biology 425, 3389-3402, doi: 10.1016/j.jmb.2013.06.029 (2013).
34. Fage, C. D., Brown, D. B., Boll, J. M., Keatinge-Clay, A. T. & Trent, M. S. Crystallographic study of the phosphoethanolamine transferase EptC required for polymyxin resistance and motility in Campylobacter jejuni. Acta Crystallogr D 70, 2730-2739, doi: 10.1107/S1399004714017623 (2014).
35. Cullen, T. W. & Trent, M. S. A link between the assembly of flagella and lipooligosaccharide of the Gram-negative bacterium Campylobacter jejuni. Proceedings of the National Academy of Sciences of the United States of America 107, 5160-5165, doi: 10.1073/pnas.0913451107 (2010).
36. Cullen, T. W., Madsen, J. A., Ivanov, P. L., Brodbelt, J. S. & Trent, M. S. Characterization of Unique Modification of Flagellar Rod Protein FlgG by Campylobacter jejuni Lipid A Phosphoethanolamine Transferase, Linking Bacterial Locomotion and Antimicrobial Peptide Resistance. Journal of Biological Chemistry 287, 3326-3336 (2012).
37. Cullen, T. W. et al. EptC of Campylobacter jejuni Mediates Phenotypes Involved in Host Interactions and Virulence. Infection and immunity 81, 430-440, doi: 10.1128/Iai.01046-12 (2013).
38. Scott, N. E. et al. Modification of the Campylobacter jejuni N-Linked Glycan by EptC Protein-mediated Addition of Phosphoethanolamine. Journal of Biological Chemistry 287, 29384-29396, doi: 10.1074/jbc.M112.380212 (2012).
39. Holm, L. & Rosenstrom, P. Dali server: conservation mapping in 3D. Nucleic acids research 38, W545-W549, doi: 10.1093/nar/gkq366 (2010).
40. Van Loo, B., Schober, M., Valkov, E., Heberlein, M., Faber, K., Hyvonen, M. & Hollfelder, F. Structural and Mechanistic Analysis of the Choline Sulfatase from Sinorhizobium Melliloti: A Class I Sulfatase Specific for an Alkyl Sulfate Ester. (To Be Published).
41. van Loo, B. et al. An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily. Proceedings of the National Academy of Sciences of the United States of America 107, 2740-2745 (2010).
42. Stojanoski, V. et al. Structure of the catalytic domain of the colistin resistance enzyme MCR-1. BMC Biol 14, 81, doi: 10.1186/s12915-016-0303-0 (2016).
43. Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta crystallographica. Section D, Biological crystallography 58, 1772-1779 (2002).
44. Jonas, S., van Loo, B., Hyvonen, M. & Hollfelder, F. A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium leguminosarum. Journal of molecular biology 384, 120-136, doi: 10.1016/j.jmb.2008.08.072 (2008).
45. Schirner, K., Marles-Wright, J., Lewis, R. J. & Errington, J. Distinct and essential morphogenic functions for wall- and lipo-teichoic acids in Bacillus subtilis. The EMBO journal 28, 830-842, doi: 10.1038/emboj.2009.25 (2009).
46. Gao, R., Wang, Q., Li, P., Li, Z. & Feng, Y. Genome sequence and characteristics of plasmid pWH12, a variant of the mcr-1-harbouring plasmid pHNSHP45, from the multi-drug resistant E. coli. Virulence 0, doi: 10.1080/21505594.2016.1193279 (2016).
47. Gao, R., Li, Y., Lin, J., Tan, C. & Feng, Y. Unexpected complexity of multidrug resistance in the mcr-1-harbouring Escherichia coli. Science China. Life sciences, doi: 10.1007/s11427-016-5070-1 (2016).
48. Takao, M. et al. A 127 Kda Component of a Uv-Damaged DNA-Binding Complex, Which Is Defective in Some Xeroderma-Pigmentosum Group-E Patients, Is Homologous to a Slime-Mold Protein. Nucleic acids research 21, 4111-4118, doi: 10.1093/nar/21.17.4111 (1993).
49. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Macromolecular Crystallography, Pt A 276, 307-326 (1997).
50. Matthews, B. W. Solvent Content of Protein Crystals. Journal of molecular biology 33, 491-&, doi: 10.1016/0022-2836(68)90205-2 (1968).
51. Panjikar, S., Parthasarathy, V., Lamzin, V. S., Weiss, M. S. & Tucker, P. A. Auto-Rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment. Acta Crystallogr D 61, 449-457, doi: 10.1107/S0907444905001307 (2005).
52. Collaborative. The CCP4 suite: programs for protein crystallography. Acta Crystallographica Section D 50, 760-763, doi: 10.1107/S0907444994003112 (1994).
53. Sheldrick, G. Macromolecular applications of SHELX. International Tables for Crystallography (Rossmann, M. G. & Arnold, E. eds), vol. F, 734-738 (2001).
54. Hao, Q. ABS: a program to determine absolute configuration and evaluate anomalous scatterer substructure. J Appl Crystallogr 37, 498-499 (2004).
55. Sheldrick, G. M. Macromolecular phasing with SHELXE. Zeitschrift für Kristallographie-Crystalline Materials 217, 644-650 (2002).
56. Perrakis, A., Morris, R. & Lamzin, V. S. Automated protein model building combined with iterative structure refinement. Nature structural & molecular biology 6, 458-463 (1999).
57. Morris, R. J. et al. Breaking good resolutions with ARP/wARP. J Synchrotron Radiat 11, 56-59 (2004).
58. Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D 58, 1948-1954 (2002).
59. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53, 240-255, doi: 10.1107/S0907444996012255 (1997).
60. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr D 60, 2126-2132 (2004).
61. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D 66, 12-21, doi: 10.1107/S0907444909042073 (2010).
62. DeLano, W. L. The PyMOL molecular graphics system (2002).