Structural insights into higher order assembly and function of the bacterial micro compartment protein PduA

Journal of Biological Chemistry

Volumn 289, Issue 32, 2014, Pages 22377-22384

  Pang, Allan ^a,c   Frank, Stefanie ^b   Brown, Ian ^b   Warren, Martin J ^b   Pickersgill, Richard W ^a  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY OF KENT   (United Kingdom)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOLOGY;

1 ,2-PROPANEDIOL; BACTERIAL CYTOPLASM; IN-VIVO; MICRO-COMPARTMENTS; NANOTUBE ASSEMBLIES; STRUCTURAL INSIGHTS; SYNTHETIC BIOLOGY;

PROTEINS;

BACTERIAL PROTEIN; PDUA PROTEIN, SALMONELLA ENTERICA; PROTEIN SUBUNIT; RECOMBINANT PROTEIN;

AMINO ACID SEQUENCE; CELL INCLUSION; CHEMICAL STRUCTURE; CHEMISTRY; CITROBACTER FREUNDII; ESCHERICHIA COLI; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN DOMAIN; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN SUBUNIT; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; STATIC ELECTRICITY; TRANSMISSION ELECTRON MICROSCOPY; ULTRASTRUCTURE; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CITROBACTER FREUNDII; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; INCLUSION BODIES; MICROSCOPY, ELECTRON, TRANSMISSION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN SUBUNITS; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; STATIC ELECTRICITY;

EID: 84905867273     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M114.569285     Document Type: Article

References (32)

1. Bobik, T. A., Havemann, G. D., Busch, R. J., Williams, D. S., and Aldrich, H. C. (1999) The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B12-dependent 1, 2-propanediol degradation. J. Bacteriol. 181, 5967-5975
2. Shively, J. M., Bradburne, C. E., Aldrich, H. C., Bobik, T. A., Mehlman, J. L., Jin, S., and Baker, S. H. (1998) Sequence homologs of the carboxysomal polypeptide CsoS1 of the thiobacilli are present in cyanobacteria and enteric bacteria that form carboxysomes: polyhedral bodies. Can. J. Bot. 76, 906-916
3. Sriramulu, D. D., Liang, M., Hernandez-Romero, D., Raux-Deery, E., Lünsdorf, H., Parsons, J. B., Warren, M. J., and Prentice, M. B. (2008) Lactobacillus reuteri DSM 20016 produces cobalamin-dependent diol dehydratase in metabolosomes and metabolizes 1,2-propanediol by disproportionation. J. Bacteriol. 190, 4559-4567
4. Bock, E., Düvel, D. and Peters, K. R. (1974) [Characterization of a phagelike particle from cells of Nitrobacter. I. Host-particle correlation and particle isolation (author's transl)]. Arch. Microbiol. 97, 115-127
5. Kerfeld, C. A., Heinhorst, S., and Cannon, G. C. (2010) Bacterial microcompartments. Annu. Rev. Microbiol. 64, 391-408
6. Brinsmade, S. R., Paldon, T., and Escalante-Semerena, J. C. (2005) Minimal functions and physiological conditions required for growth of Salmonella enterica on ethanolamine in the absence of the metabolosome. J. Bacteriol. 187, 8039-8046
7. Jorda, J., Lopez, D., Wheatley, N. M., and Yeates, T. O. (2013) Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria. Protein Sci. 22, 179-195
8. Seedorf, H., Fricke, W. F., Veith, B., Brüggemann, H., Liesegang, H., Strittmatter, A., Miethke, M., Buckel, W., Hinderberger, J., Li, F., Hagemeier, C., Thauer, R. K., and Gottschalk, G. (2008) The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc. Natl. Acad. Sci. U.S.A. 105, 2128-2133
9. Stojiljkovic, I., Bäumler, A. J. and Heffron, F. (1995) Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster. J. Bacteriol. 177, 1357-1366
10. Walter, D., Ailion, M., and Roth, J. (1997) Genetic characterization of the pdu operon: use of 1,2-propanediol in Salmonella typhimurium. J. Bacteriol. 179, 1013-1022
11. Kerfeld, C. A., Sawaya, M. R., Tanaka, S., Nguyen, C. V., Phillips, M., Beeby, M., Yeates, T. O. (2005) Protein structures forming the shell of primitive bacterial organelles. Science 309, 936-938
12. Heldt, D., Frank, S., Seyedarabi, A., Ladikis, D., Parsons, J. B., Warren, M. J., and Pickersgill, R. W. (2009) Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri. Biochem. J. 423, 199-207
13. Yeates, T. O., Kerfeld, C. A., Heinhorst, S., Cannon, G. C., and Shively, J. M. (2008) Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat. Rev. Microbiol. 6, 681-691
14. Pang, A., Warren, M. J., and Pickersgill, R. W. (2011) Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe-4S cluster-binding site. Acta Crystallogr. D Biol. Crystallogr. 67, 91-96
15. Havemann, G. D., and Bobik, T. A. (2003) Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2. J. Bacteriol. 185, 5086-5095
16. Parsons, J. B., Dinesh, S. D., Deery, E., Leech, H. K., Brindley, A. A., Heldt, D., Frank, S., Smales, C. M., Lünsdorf, H., Rambach, A., Gass, M. H., Bleloch, A., McClean, K. J., Munro, A. W., Rigby, S. E., Warren, M. J., and Prentice, M. B. (2008) Biochemical and structural insights into bacterial organelle form and biogenesis. J. Biol. Chem. 283, 14366-14375
17. Parsons, J. B., Frank, S., Bhella, D., Liang, M., Prentice, M. B., Mulvihill, D. P., Warren, M. J. (2010) Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filamentassociated organelle movement. Mol. Cell 38, 305-315
18. Cheng, S., Sinha, S., Fan, C., Liu, Y., and Bobik, T. A. (2011) Genetic analysis of the protein shell of the microcompartments involved in coenzyme B-12-dependent 1,2-propanediol degradation by Salmonella. J. Bacteriol. 193, 1385-1392
19. Crowley, C. S., Cascio, D., Sawaya, M. R., Kopstein, J. S., Bobik, T. A., and Yeates, T. O. (2010) Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J. Biol. Chem. 285, 37838-37846
20. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr.DBiol. Crystallogr. 50, 760-763
21. DeLano, W. L., and Lam, J. W. (2005) PyMOL: a communications tool for computational models. Abstr. Papers Am. Chem. Soc. 230, 254-COMP
22. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. (2007) ClustalW and ClustalX version 2.0. Bioinformatics 23, 2947-2948
23. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., and Wolfson, H. J. (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 33, W363-W367
24. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., and Wolfson, H. J. (2005) Geometry-based flexible and symmetric protein docking. Proteins 60, 224-231
25. Kabsch, W., (2010) XDS. Acta Crystallogr.DBiol. Crystallogr. 66, 125-132
26. Evans, P. (2006) Scaling and assessment of data quality. Acta Crystallogr.D Biol. Crystallogr. 62, 72-82
27. Vagin, A., and Teplyakov, A. (1997) MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022-1025
28. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
29. Emsley, P., Lohkamp, B., Scott, W. G., and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501
30. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) Procheck: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291
31. Pang, A., Liang, M., Prentice, M. B., and Pickersgill, R. W. (2012) Substrate channels revealed in the trimeric Lactobacillus reuteri bacterial microcompartment shell protein PduB. Acta Crystallogr. D Biol. Crystallogr. 68, 1642-1652
32. Frank, S., Lawrence, A. D., Prentice, M. B., and Warren, M. J. (2013) Bacterial microcompartments moving into a synthetic biological world. J. Biotechnol. 163, 273-279