Comparative analysis of amino acid composition in the active site of nirk gene encoding copper-containing nitrite reductase (CuNiR) in bacterial spp.

Abraham, 1993, Purification and characterization of the dissimilatory nitrite reductase from Alcaligenes xylosoxidans subsp. xylosoxidans (N.C.I.M.B11015): evidence for the presence of both type 1 and type 2 copper centres, Biochem. J., 295, 587, 10.1042/bj2950587 Adman, 1995, The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted, J. Biol. Chem., 270, 27458, 10.1074/jbc.270.46.27458 Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 Antonyuk, 2005, Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism, Proc. Natl. Acad. Sci. U. S. A., 102, 12041, 10.1073/pnas.0504207102 Averill, 1996, Dissimilatory nitrite and nitric oxide reductases, Chem. Rev., 96, 2951, 10.1021/cr950056p Aylott, 1997, Optical biosensing of nitrate ions using a sol-Gel immobilized nitrate reductase, Analyst, 122, 77, 10.1039/a606146j Biasini, 2014, SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information, Nucleic Acids Res., 42, W252, 10.1093/nar/gku340 Boulanger, 2001, Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate, Biochemistry, 40, 9132, 10.1021/bi0107400 Boulanger, 2002, Crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria: a new class of copper-containing nitrite reductases, J. Mol. Biol., 315, 1111, 10.1006/jmbi.2001.5251 Boulanger, 2000, Catalytic roles for two water bridged residues (Asp-98 and his-255) in the active site of copper-containing nitrite reductase, J. Biol. Chem., 275, 23957, 10.1074/jbc.M001859200 Cabello, 2004, Nitrate reduction and the nitrogen cycle in archaea, Microbiology, 150, 3527, 10.1099/mic.0.27303-0 Castrignanò, 2006, The PMDB protein model database, Nucleic Acids Res., 34, D306, 10.1093/nar/gkj105 Chen, 2009, A nitrite biosensor based on the immobilization of cytochrome c on multi-walled carbon nanotubes-PAMAM-chitosan nanocomposite modified glass carbon electrode, Biosens. Bioelectron., 24, 2991, 10.1016/j.bios.2009.03.007 Colovos, 1993, Verification of protein structures: patterns of nonbonded atomic interactions, Protein Sci., 2, 1511, 10.1002/pro.5560020916 Coyne, 1990, Localization of the cytochrome cd1 and copper nitrite reductases in denitrifying bacteria, J. Bacteriol., 172, 2558, 10.1128/jb.172.5.2558-2562.1990 Dodd, 1997, Structures of a blue-copper nitrite reductase and its substrate-bound complex, Acta Crystallogr. D. Biol. Crystallogr., 53, 406, 10.1107/S0907444997002667 Dundas, 2006, CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues, Nucleic Acids Res., 34, W116, 10.1093/nar/gkl282 Dunker, 2001, The protein trinity?linking function and disorder, Nat. Biotechnol., 19, 805, 10.1038/nbt0901-805 Dyson, 2005, Intrinsically unstructured proteins and their functions, Nat. Rev. Mol. Cell Biol., 6, 197, 10.1038/nrm1589 Eisenberg, 1997, VERIFY3D: assessment of protein models with three-dimensional profiles, Methods Enzymol., 277, 396, 10.1016/S0076-6879(97)77022-8 Ellis, 2002, Biochemical and crystallographic studies of the Met144Ala, Asp92Asn and His254Phe mutants of the nitrite reductase from Alcaligenes xylosoxidans provide insight into the enzyme mechanism, J. Mol. Biol., 316, 51, 10.1006/jmbi.2001.5304 Fülöp, 1995, The anatomy of a bifunctional enzyme: structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1, Cell, 81, 369, 10.1016/0092-8674(95)90390-9 Fenderson, 1991, Amino acid sequence of nitrite reductase: a copper protein from Achromobacter cycloclastes, Biochemistry, 30, 7180, 10.1021/bi00243a020 Guex, 1997, SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling, Electrophoresis, 18, 2714, 10.1002/elps.1150181505 Hoffmann, 1998, Ammonification in Bacillus subtilis utilizing dissimilatory nitrite reductase is dependent on resDE, J. Bacteriol., 180, 186, 10.1128/JB.180.1.186-189.1998 Inatomi, 1996, The purification and properties of a copper nitrite reductase from Haloferax denitrificans, Curr. Microbiol., 32, 72, 10.1007/s002849900013 Inoue, 1998, Type 1 Cu structure of blue nitrite reductase from Alcaligenes xylosoxidans GIFU 1051 at 2.05 A resolution: comparison of blue and green nitrite reductases, J. Biochem., 124, 876, 10.1093/oxfordjournals.jbchem.a022201 Ishida, 2008, Prediction of disordered regions in proteins based on the meta approach, Bioinformatics, 24, 1344, 10.1093/bioinformatics/btn195 Jacobson, 2007, pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase, J. Biol. Chem., 282, 6347, 10.1074/jbc.M605746200 Jeanmougin, 1998, Multiple sequence alignment with clustal x, Trends Biochem. Sci., 23, 403, 10.1016/S0968-0004(98)01285-7 Körner, 1992, Periplasmic location of nitrous oxide reductase and its apoform in denitrifying Pseudomonas stutzeri, Arch. Microbiol., 157, 218, 10.1007/BF00245153 Kataoka, 2000, Functional analysis of conserved aspartate and histidine residues located around the type 2 copper site of copper-containing nitrite reductase, J. Biochem., 127, 345, 10.1093/oxfordjournals.jbchem.a022613 Kim, 2009, Eukaryotic nirK genes encoding copper-Containing nitrite reductase: originating from the protomitochondrion?, Appl. Environ. Microbiol., 75, 2652, 10.1128/AEM.02536-08 Kobayashi, 1995, The copper-containing dissimilatory nitrite reductase involved in the denitrifying system of the fungus Fusarium oxysporum, J. Biol. Chem., 10.1074/jbc.270.8.4146 Kukimoto, 1994, X-ray structure and site-directed mutagenesis of a nitrite reductase from Alcaligenes faecalis S-6: roles of two copper atoms in nitrite reduction, Biochemistry, 33, 5246, 10.1021/bi00183a030 Laskowski, 1996, AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR, J. Biomol. NMR, 8, 477, 10.1007/BF00228148 Laskowski, 2005, PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids, Nucleic Acids Res., 33, D266, 10.1093/nar/gki001 Leferink, 2014, Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase, Nat. Commun., 5, 1, 10.1038/ncomms5395 Lehnert, 2007, Synthesis and spectroscopic characterization of copper(II)-nitrito complexes with hydrotris(pyrazolyl)borate and related coligands, Inorg. Chem., 46, 3916, 10.1021/ic0619355 Li, 2004, pH-profile crystal structure studies of C-terminal despentapeptide nitrite reductase from Achromobacter cycloclastes, Biochem. Biophys. Res. Commun., 316, 107, 10.1016/j.bbrc.2004.01.177 Li, 2015, Enzymatic mechanism of copper-Containing nitrite reductase, Biochemistry, 54, 1233, 10.1021/bi5007767 Liang, 1998, Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design, Protein Sci., 7, 1884, 10.1002/pro.5560070905 Libby, 1992, Evidence that the type 2 copper centers are the site of nitrite reduction by Achromobacter cycloclastes nitrite reductase, Biochem. Biophys. Res. Commun., 187, 1529, 10.1016/0006-291X(92)90476-2 Linding, 2003, GlobPlot: exploring protein sequences for globularity and disorder, Nucleic Acids Res., 31, 3701, 10.1093/nar/gkg519 Luthy, 1992, Assessment of protein models with three-dimensional profiles, Nature, 356, 83, 10.1038/356083a0 MacPherson, 2007, Type-2 copper-containing enzymes, Cell. Mol. Life Sci., 64, 2887, 10.1007/s00018-007-7310-9 Melo, 1998, Assessing protein structures with a non-local atomic interaction energy, J. Mol. Biol., 277, 1141, 10.1006/jmbi.1998.1665 Morris, 1992, Stereochemical quality of protein structure coordinates, Proteins Struct. Funct. Genet., 12, 345, 10.1002/prot.340120407 Murphy, 1997, Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications, J. Biol. Chem., 272, 28455, 10.1074/jbc.272.45.28455 Murvai, 2001, The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments, Nucleic Acids Res., 29, 58, 10.1093/nar/29.1.58 Nakanishi, 2010, A eukaryotic copper-Containing nitrite reductase derived from a NirK homolog gene of Aspergillus oryzae, Biosci. Biotechnol. Biochem., 74, 984, 10.1271/bbb.90844 Obradovic, 2005, Exploiting heterogeneous sequence properties improves prediction of protein disorder, Proteins, 61, 176, 10.1002/prot.20735 Oldfield, 2005, Addressing the intrinsic disorder bottleneck in structural proteomics, Proteins, 59, 444, 10.1002/prot.20446 Orosz, 2011, Proteins without 3D structure: definition, detection and beyond, Bioinformatics, 27, 1449, 10.1093/bioinformatics/btr175 Ramachandran, 1963, Stereochemistry of polypeptide chain configurations, J. Mol. Biol., 7, 95, 10.1016/S0022-2836(63)80023-6 Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406 Sali, 1993, Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol., 234, 779, 10.1006/jmbi.1993.1626 Seib, 2006, Defenses against oxidative stress in Neisseria gonorrhoeae: a system tailored for a challenging environment, Microbiol. Mol. Biol. Rev., 70, 344, 10.1128/MMBR.00044-05 Shen, 2006, Statistical potential for assessment and prediction of protein structures, Protein Sci., 15, 2507, 10.1110/ps.062416606 Tamura, 2013, MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30, 2725, 10.1093/molbev/mst197 Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673 Tocheva, 2004, Side-on copper-nitrosyl coordination by nitrite reductase, Science, 304, 867, 10.1126/science.1095109 Usov, 2006, EPR-ENDOR of the Cu(I)NO complex of nitrite reductase, J. Am. Chem. Soc., 128, 13102, 10.1021/ja056166n Webb, 2014, Comparative protein structure modeling using MODELLER, Curr. Protoc. Bioinforma., 47, 10.1002/0471250953.bi0506s47 Wiederstein, 2007, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Res., 35, W407, 10.1093/nar/gkm290 Wu, 1997, A nitrite biosensor based on a maltose binding protein nitrite reductase fusion immobilized on an electropolymerized film of a pyrrole-derived bipyridinium, Anal. Chem., 69, 4856, 10.1021/ac970595p Yokoyama, 2005, CuI and CuII complexes containing nitrite and tridentate aromatic amine ligand as models for the substrate-Binding type-2 Cu site of nitrite reductase, Eur. J. Inorg. Chem., 2005, 1435, 10.1002/ejic.200400808 Zhang, 2000, Carbon monoxide binding to copper-Containing nitrite reductase from alcaligenes faecalis, J. Phys. Chem. B, 104, 10738, 10.1021/jp000745r Zumft, 1997, Cell biology and molecular basis of denitrification, Microbiol. Mol. Biol. Rev., 61, 533