Structural conservation of the B subunit in the ammonia monooxygenase/particulate methane monooxygenase superfamily

Proteins: Structure, Function and Bioinformatics

Volumn 82, Issue 9, 2014, Pages 2263-2267

  Lawton, Thomas J ^a   Ham, Jungwha ^a   Sun, Tianlin ^a   Rosenzweig, Amy C ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

AMO; AmoB; Copper; Crystal structure; Cupredoxin; Hydrocarbon monooxygenase; Methanotroph; PMMO

Indexed keywords

AMMONIA MONOOXYGENASE; METHANE MONOOXYGENASE; PARTICULATE METHANE MONOOXYGENASE; SIGNAL PEPTIDE; UNCLASSIFIED DRUG; UNSPECIFIC MONOOXYGENASE; AZURIN; COPPER; CUPREDOXIN; OXIDOREDUCTASE; OXYGENASE; PROTEIN BINDING;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; CYTOPLASM; DISULFIDE BOND; METHANOTROPHIC BACTERIUM; METHYLOCOCCUS CAPSULATUS; METHYLOSINUS TRICHOSPORIUM; NITROSOCALDUS YELLOWSTONII; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; PROTEIN SUBUNIT; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; CRENARCHAEOTA; ENZYME ACTIVE SITE; ENZYMOLOGY; MOLECULAR GENETICS; PROTEIN FOLDING; ULTRASTRUCTURE; X RAY CRYSTALLOGRAPHY;

ARCHAEA;

AMINO ACID SEQUENCE; AZURIN; BINDING SITES; CATALYTIC DOMAIN; COPPER; CRENARCHAEOTA; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES; OXYGENASES; PROTEIN BINDING; PROTEIN FOLDING;

EID: 84906309293     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24535     Document Type: Article

References (25)

1. Tavormina PL, Orphan VJ, Kalyuzhnaya MG, Jetten MSM, Klotz MG. A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. Environ Microbiol Rep 2011;3:91-100.
2. Arp DJ, Sayavedra-Soto LA, Hommes NG. Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch Microbiol 2002;178:250-255.
3. Hakemian AS, Rosenzweig AC. The biochemistry of methane oxidation. Ann Rev Biochem 2007;76:223-241.
4. Hanson RS, Hanson TE. Methanotrophic bacteria. Microbiol Rev 1996;60:439-471.
5. Koops H-P, Purkhold U, Pommerening-Röser A, Timmermann G, Wagner M. The lithoautotrophic ammonia-oxidizing bacteria. Prokaryotes 2006;5:778-811.
6. Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PSG, Chan PP, Gollabgir A, Hemp J, Hugler M, Karr EA, Konneke M, Shin M, Lawton TJ, Lowe T, Martens-Habbena W, Sayavedra-Soto LA, Lang D, Sievert SM, Rosenzweig AC, Manning G, Stahl DA. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 2010;107:8818-8823.
7. de la Torre JR, Walker CB, Ingalls AE, Konneke M, Stahl DA. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 2008;10:810-818.
8. Sayavedra-Soto LA, Hamamura N, Liu CW, Kimbrel JA, Chang JH, Arp DJ. The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family. Environ Microbiol Rep 2011;3:390-396.
9. Coleman NV, Le NB, Ly MA, Ogawa HE, McCarl V, Lwilson N, Holmes AJ. Hydrocarbon monooxygenase in Mycobacterium: recombinant expression of a member of the ammonia monooxygenase superfamily. ISME J 2012;6:171-182.
10. Coleman NV, Yau S, Wilson NL, Nolan LM, Migocki MD, Ly MA, Crossett B, Holmes AJ. Untangling the multiple monooxygenases of Mycobacterium chubuense strain NBB4, a versatile hydrocarbon degrader. Environ Microbiol Rep 2011;3:297-307.
11. Redmond MC, Valentine DL, Sessions AL. Identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing. Appl Environ Microbiol 2010;76:6412-6422.
12. Suzuki T, Nakamura T, Fuse H. Isolation of two novel marine ethylene-assimilating bacteria, Haliea species ETY-M and ETY-NAG, containing particulate methane monooxygenase-like genes. Microbes Environ 2012;27:54-60.
13. Lieberman RL, Rosenzweig AC. Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane. Nature 2005;434:177-182.
14. Hakemian AS, Kondapalli KC, Telser J, Hoffman BM, Stemmler TL, Rosenzweig AC. The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b. Biochemistry 2008; 47:6793-6801.
15. Smith SM, Rawat S, Telser J, Hoffman BM, Stemmler TL, Rosenzweig AC. Crystal structure and characterization of particulate methane monooxygenase from Methylocystis species strain M. Biochemistry 2011;50:10231-10240.
16. Balasubramanian R, Smith SM, Rawat S, Stemmler TL, Rosenzweig AC. Oxidation of methane by a biological dicopper centre. Nature 2010;465:115-119.
17. Culpepper MA, Cutsail GE, Hoffman BM, Rosenzweig AC. Evidence for oxygen binding at the active site of particulate methane monooxygenase. J Am Chem Soc 2012;134:7640-7643.
18. Culpepper MA, Rosenzweig AC. Architecture and active site of particulate methane monooxygenase. Crit Rev Biochem Mol Biol 2012;47:483-492.
19. Op den Camp HJ, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM, Birkeland N-K, Pol A, Dunfield PF. Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ Microbiol Rep 2009;1:293-306.
20. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997;276:307-326.
21. Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Cryst 2010;D66:486-501.
22. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst 1997;D53:240-255.
23. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Cryst 2007;40:658-674.
24. Krissinel E, Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Cryst 2004;D60(12 Pt 1):2256-2268.
25. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 2000;16:276-277.