Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution.
Nitroaromatic compounds are typically toxic and resistant to degradation. Bradyrhizobium species strain JS329 metabolizes 5-nitroanthranilic acid (5NAA), which is a molecule secreted by Streptomyces scabies, the plant pathogen responsible for potato scab. The first biodegradation enzyme is 5NAA-aminohydrolase (5NAA-A), a metalloprotease family member that converts 5NAA to 5-nitrosalicylic acid. We characterized 5NAA-A biochemically and obtained snapshots of its mechanism. 5NAA-A, an octamer that can use several divalent transition metals for catalysis in vitro, employs a nucleophilic aromatic substitution mechanism. Unexpectedly, the metal in 5NAA-A is labile but is readily loaded in the presence of substrate. 5NAA-A is specific for 5NAA and cannot hydrolyze other tested derivatives, which are likewise poor inhibitors. The 5NAA-A structure and mechanism expand our understanding of the chemical ecology of an agriculturally important plant and pathogen, and will inform bioremediation and biocatalytic approaches to mitigate the environmental and ecological impact of nitroanilines and other challenging substrates.
School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA.
Sibel
S
Kalyoncu
School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA.
David P
DP
Heaner
School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA.
Zohre
Z
Kurt
School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA.
Casey M
CM
Bethel
School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA.
Chiamaka U
CU
Ukachukwu
Biophysics Collaborative Access Team, Advanced Photon Source, Argonne National Labs, Lemont, IL.
Srinivas
S
Chakravarthy
School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA.|Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL.
Jim C
JC
Spain
School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA.
Raquel L
RL
Lieberman
D000619:Aminohydrolases / Q000737:chemistry / Q000378:metabolism*; D001463:Barbiturates / Q000737:chemistry / Q000378:metabolism; D002384:Catalysis; D006868:Hydrolysis / Q000187:drug effects; D008958:Models, Molecular; D015394:Molecular Structure; D009574:Nitro Compounds / Q000737:chemistry / Q000494:pharmacology*; D009942:Organometallic Compounds / Q000737:chemistry / Q000494:pharmacology*; D012459:Salicylates / Q000737:chemistry / Q000378:metabolism; D028561:Transition Elements / Q000737:chemistry / Q000494:pharmacology*
D001463:Barbiturates; D009574:Nitro Compounds; D009942:Organometallic Compounds; D012459:Salicylates; D028561:Transition Elements; C022044:5-nitrobarbituric acid; D000619:Aminohydrolases
Biochemistry. 2011 Oct 4;50(39):8264-9
21888353
Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601
19465773
J Biol Chem. 1999 Jun 18;274(25):17395-8
10364165
J Mol Biol. 2010 Apr 2;397(3):617-26
20138056
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
20124702
Annu Rev Microbiol. 1995;49:523-55
8561470
PLoS One. 2011 Jan 24;6(1):e16347
21283635
Int J Environ Res Public Health. 2009 Aug;6(8):2226-47
19742157
Gene. 1992 Jul 1;116(1):1-6
1628835
Chembiochem. 2007 Jun 18;8(9):973-7
17477464
Mol Plant Pathol. 2009 Sep;10(5):579-85
19694949
Anal Biochem. 1990 Jun;187(2):328-36
2116741
Nat Prod Rep. 2006 Dec;23(6):845-50
17119634
Microbiol Mol Biol Rev. 2010 Jun;74(2):250-72
20508249
J Bacteriol. 2012 Nov;194(21):5759-68
22904279
Chem Rev. 2009 Oct;109(10):4682-707
19728700
Biophys J. 1999 Jun;76(6):2879-86
10354416
J Bacteriol. 2011 Jun;193(12):3057-63
21498645
Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1074-80
19770504
J Biomed Opt. 2011 Aug;16(8):087011
21895338
Appl Environ Microbiol. 2005 Sep;71(9):4951-9
16151072
Methods Enzymol. 1997;276:307-26
27754618
Nature. 2010 Aug 5;466(7307):779-82
20639861
PLoS Comput Biol. 2012;8(10):e1002708
23093919
J Biol Inorg Chem. 2002 Mar;7(3):284-98
11935352
Appl Environ Microbiol. 2010 Mar;76(5):1417-22
20081004
Nat Protoc. 2015 May;10(5):733-55
25855957
Microbes Environ. 2015;30(4):301-9
26657303
Phytochemistry. 2009 May;70(7):833-41
19467551
J Biol Chem. 2014 Oct 10;289(41):28095-103
25160626
Nucleic Acids Res. 2003 Jul 1;31(13):3381-5
12824332
J Mol Biol. 2007 Sep 21;372(3):774-97
17681537
Annu Rev Biochem. 2001;70:209-46
11395407
Biochemistry. 2011 May 31;50(21):4402-10
21506553
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
20383002
Biochemistry. 1979 Apr 3;18(7):1230-8
218617
Chem Rev. 2001 Aug;101(8):2271-90
11749373
Mol Biol Evol. 2013 Dec;30(12):2725-9
24132122
Nat Prod Rep. 2011 Jan;28(1):152-67
21127810
Biophys Chem. 2007 Mar;126(1-3):86-93
16750290
Int J Syst Bacteriol. 1997 Oct;47(4):969-74
9336894
Structure. 1997 Mar 15;5(3):337-47
9083113
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
19461840
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600
23671338
J Appl Crystallogr. 2009 Apr 1;42(Pt 2):342-346
27630371
J Biotechnol. 2007 Mar 30;129(1):3-5
17208324
Genome Biol. 2007;8(3):R31
17335583
Nat Struct Mol Biol. 2007 Jan;14(1):7-9
17203067
FEMS Microbiol Ecol. 2011 Mar;75(3):351-64
21204870
Antioxid Redox Signal. 2013 Sep 20;19(9):933-44
23249283
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
15034147
J Mol Biol. 1999 Sep 10;292(1):11-7
10493853
Comput Appl Biosci. 1992 Jun;8(3):275-82
1633570