Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 29, 2012, Pages 11812-11817

  Arbing, Mark A ^a   Chan, Sum ^a   Shin, Annie ^a   Phan, Tung ^a   Ahn, Christine J ^a   Rohlin, Lars ^a   Gunsalus, Robert P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Domain of unknown function 1608; Methanogen; S layer structure; Surface layer protein; X ray crystallography

Indexed keywords

BACTERIAL PROTEIN; NANOMATERIAL; POLYPEPTIDE; VIRUS ENVELOPE PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; CYTOPLASM; ELECTRON MICROSCOPY; EUKARYOTE; METHANOGENIC ARCHAEON; METHANOSARCINA ACETIVORANS; MOLECULAR MODEL; NONHUMAN; NUTRIENT; POROSITY; PRIORITY JOURNAL; PROTEIN DOMAIN; SURFACE PROPERTY; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; EVOLUTION, MOLECULAR; MEMBRANE GLYCOPROTEINS; METHANOSARCINA; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION;

EUKARYOTA; METHANOSARCINA ACETIVORANS;

EID: 84863939189     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1120595109     Document Type: Article

References (42)

1. Koenig H (1988) Archaeobacterial cell envelopes. Can J Microbiol 34:395-406.
2. Sleytr UB, Messner P (1983) Crystalline surface layers on bacteria. Annu Rev Microbiol 37:311-339.
3. Sleytr UB, Egelseer EM, Ilk N, Pum D, Schuster B (2007) S-Layers as a basic building block in a molecular construction kit. FEBS J 274:323-334. (Pubitemid 46046643)
4. Engelhardt H (2007) Mechanism of osmoprotection by archaeal S-layers: A theoretical study. J Struct Biol 160:190-199.
5. Fagan RP, et al. (2009) Structural insights into the molecular organization of the S-layer from Clostridium difficile. Mol Microbiol 71:1308-1322.
6. Kern J, et al. (2011) Structure of surface layer homology (SLH) domains from Bacillus anthracis surface array protein. J Biol Chem 286:26042-26049.
7. Pavkov T, et al. (2008) The structure and binding behavior of the bacterial cell surface layer protein SbsC. Structure 16:1226-1237.
8. Jing H, et al. (2002) Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related tometazoan cell surface proteins. Structure 10:1453-1464. (Pubitemid 35232388)
9. Francoleon DR, et al. (2009) S-layer, surface-accessible, and concanavalin A binding proteins of Methanosarcina acetivorans and Methanosarcina mazei. J Proteome Res 8:1972-1982.
10. Sowers KR, Boone JE, Gunsalus RP (1993) Disaggregation of Methanosarcina spp. and Growth as Single Cells at Elevated Osmolarity. Appl Environ Microbiol 59:3832-3839. (Pubitemid 23327589)
11. Finn RD, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38(Database issue):D211-D222.
12. Rohlin L, et al. (2012) Identification of the major expressed S-layer and cell surface layer related proteins in the model methanogenic archaea, Methanosarcina barkeri Fusaro and Methanosarcina acetivorans C2A. Archaea 2012, 873589.
13. Houwink AL (1953) A macromolecular mono-layer in the cell wall of Spirillum spec. Biochim Biophys Acta 10:360-366.
14. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774-797. (Pubitemid 47321791)
15. Lawrence MC, Colman PM (1993) Shape complementarity at protein/protein interfaces. J Mol Biol 234:946-950. (Pubitemid 24027225)
16. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38(Web Server issue):W529-W533.
17. Kelley LA, Sternberg MJ (2009) Protein structure prediction on the Web: A case study using the Phyre server. Nat Protoc 4:363-371.
18. Cheong G-W, Guckenberger R, Fuchs K-H, Gross H, Baumeister W (1993) The structure of the surface layer of Methanoplanus limicola obtained by a combined electron microscopy and scanning tunneling microscopy approach. J Struct Biol 111:125-134. (Pubitemid 24065285)
19. Trachtenberg S, Pinnick B, Kessel M (2000) The cell surface glycoprotein layer of the extreme halophile Halobacterium salinarum and its relation to Haloferax volcanii: Cryo-electron tomography of freeze-substituted cells and projection studies of negatively stained envelopes. J Struct Biol 130:10-26. (Pubitemid 30470793)
20. Cheong G-W, Cejka Z, Peters J, Stetter KO, Baumeister W (1991) The surface protein layer of Methanoplanus limicola: Three-dimensional structure and chemical characterization. Syst Appl Microbiol 14:209-217.
21. Kessel M, Wildhaber I, Cohen S, Baumeister W (1988) Three-dimensional structure of the regular surface glycoprotein layer of Halobacterium volcanii from the Dead Sea. EMBO J 7:1549-1554.
22. Saunders NF, et al. (2006) Proteomic and computational analysis of secreted proteins with type I signal peptides from the Antarctic archaeon Methanococcoides burtonii. J Proteome Res 5:2457-2464. (Pubitemid 44330840)
23. Veith A, et al. (2009) Acidianus, Sulfolobus and Metallosphaera surface layers: Structure, composition and gene expression. Mol Microbiol 73:58-72.
24. Lescar J, et al. (2001) The Fusion glycoprotein shell of Semliki Forest virus: An icosahedral assembly primed for fusogenic activation at endosomal pH. Cell 105:137-148. (Pubitemid 32323923)
25. Rey FA, Heinz FX, Mandl C, Kunz C, Harrison SC (1995) The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution. Nature 375:291-298.
26. Kuhn RJ, et al. (2002) Structure of dengue virus: Implications for flavivirus organization, maturation, and fusion. Cell 108:717-725. (Pubitemid 34241430)
27. Mukhopadhyay S, Kim BS, Chipman PR, Rossmann MG, Kuhn RJ (2003) Structure of West Nile virus. Science 302:248. (Pubitemid 37248748)
28. Mukhopadhyay S, Kuhn RJ, Rossmann MG (2005) A structural perspective of the flavivirus life cycle. Nat Rev Microbiol 3:13-22. (Pubitemid 40028466)
29. Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41:207-234.
30. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326. (Pubitemid 27085611)
31. Pape T, Schneider TR (2004) HKL2MAP: A graphical user interface for macromolecular phasing with SHELX programs. J Appl Crystallogr 37:843-844.
32. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112-122.
33. Langer G, Cohen SX, Lamzin VS, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3:1171-1179.
34. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126-2132. (Pubitemid 41742764)
35. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240-255. (Pubitemid 27235885)
36. Painter J, Merritt EA (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D Biol Crystallogr 62:439-450.
37. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760-763.
38. McCoy AJ, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40:658-674. (Pubitemid 47080256)
39. Holm L, Kääriäinen S, Rosenström P, Schenkel A (2008) Searching protein structure databases with DaliLite v.3. Bioinformatics 24:2780-2781. (Pubitemid 352722625)
40. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci USA 98: 10037-10041. (Pubitemid 32802969)
41. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA (2004) PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32(Web Server issue):W665-W667.
42. Smart OS, Neduvelil JG, Wang X, Wallace BA, Sansom MS (1996) HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph 14:354-360, 376.