Genome Property Definition Page

AccessionGenProp0200
Nameperiplasmic nitrate reductase
TypeSYSTEM
DescriptionDenitrifying bacteria reduce nitrate via three distinct nitrate reductase systems. Two of these are assciated with energy-conserving electron transport systems, distinguished by cellular location and generation of a proton motive force, and the other with nitrate assimilation. All three types involve binding of molybdopterin to the active site of nitrate reductase where reduction occurs. Unlike membrane-associated nitrate reductases, periplasmic nitrate reductase cannot itself act as a coupling site for proton translocation, but can participate indirectly in respiration by virtue of the consumption of electrons derived from NADH via the proton translocating NADH dehydrogenase. Expressed aerobically as well as anearobically in gram-negative bacteria, periplasmic nitrate reductase is a two-subunit enzyme comprised of a catalytic subunit binding molybdopterin and containing a twin-arginine signal motif, and a cytochrome subunit, whose redox partner is a membrane-bound electron transfer protein. Other essential components for this denitrifying system include a proposed chaperone, and at least five other components identified in different combinations in different bacteria [1]. Lacking the membrane-bound c-type cytochrome component, in Wolinella succinogenes electron transport to nitrate reductase from one or more of these other gene products has been demonstrated [2].
JCVI RoleNitrogen metabolism
Parent PropertyGenProp0202: nitrogen metabolism
GenProp0202: nitrogen metabolism
GenProp0202: nitrogen metabolism
Literature References
[ 1 ]Potter L, Angove H, Richardson D, Cole J.  Nitrate reduction in the periplasm of gram-negative bacteria.  Adv Microb Physiol. 2001;45:51-112.  PMID 11450112
[ 2 ]Simon J, Sanger M, Schuster SC, Gross R.  Electron transport to periplasmic nitrate reductase (NapA) of Wolinella succinogenes is independent of a NapC protein.  Mol Microbiol. 2003 Jul;49(1):69-79.  PMID 12823811
[ 3 ] Brondijk TH, Nilavongse A, Filenko N, Richardson DJ, Cole JA   NapGH components of the periplasmic nitrate reductase of Escherichia coli K-12: location, topology and physiological roles in quinol oxidation and redox balancing.   Biochem J. 2004 Apr 1;379(Pt 1):47-55.  PMID 14674886
[ 4 ] Maillard J, Spronk CA, Buchanan G, Lyall V, Richardson DJ, Palmer T, Vuister GW, Sargent F   Structural diversity in twin-arginine signal peptide-binding proteins.   Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15641-6.  PMID 17901208
[ 1 ]Potter L, Angove H, Richardson D, Cole J.  Nitrate reduction in the periplasm of gram-negative bacteria.  Adv Microb Physiol. 2001;45:51-112.  PMID 11450112
[ 2 ]Simon J, Sanger M, Schuster SC, Gross R.  Electron transport to periplasmic nitrate reductase (NapA) of Wolinella succinogenes is independent of a NapC protein.  Mol Microbiol. 2003 Jul;49(1):69-79.  PMID 12823811
[ 3 ] Brondijk TH, Nilavongse A, Filenko N, Richardson DJ, Cole JA   NapGH components of the periplasmic nitrate reductase of Escherichia coli K-12: location, topology and physiological roles in quinol oxidation and redox balancing.   Biochem J. 2004 Apr 1;379(Pt 1):47-55.  PMID 14674886
[ 4 ] Maillard J, Spronk CA, Buchanan G, Lyall V, Richardson DJ, Palmer T, Vuister GW, Sargent F   Structural diversity in twin-arginine signal peptide-binding proteins.   Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15641-6.  PMID 17901208
[ 1 ]Potter L, Angove H, Richardson D, Cole J.  Nitrate reduction in the periplasm of gram-negative bacteria.  Adv Microb Physiol. 2001;45:51-112.  PMID 11450112
[ 2 ]Simon J, Sanger M, Schuster SC, Gross R.  Electron transport to periplasmic nitrate reductase (NapA) of Wolinella succinogenes is independent of a NapC protein.  Mol Microbiol. 2003 Jul;49(1):69-79.  PMID 12823811
[ 3 ] Brondijk TH, Nilavongse A, Filenko N, Richardson DJ, Cole JA   NapGH components of the periplasmic nitrate reductase of Escherichia coli K-12: location, topology and physiological roles in quinol oxidation and redox balancing.   Biochem J. 2004 Apr 1;379(Pt 1):47-55.  PMID 14674886
[ 4 ] Maillard J, Spronk CA, Buchanan G, Lyall V, Richardson DJ, Palmer T, Vuister GW, Sargent F   Structural diversity in twin-arginine signal peptide-binding proteins.   Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15641-6.  PMID 17901208
Web ReferencesKEGG: Nitrogen metabolism
The Ecocyc Database: nitrate reductase, periplasmic
KEGG: Nitrogen metabolism
The Ecocyc Database: nitrate reductase, periplasmic
KEGG: Nitrogen metabolism
The Ecocyc Database: nitrate reductase, periplasmic
Gene Ontology TermGO:0042126: nitrate metabolic process (biological_process)
GO:0042126: nitrate metabolic process (biological_process)
GO:0042126: nitrate metabolic process (biological_process)
GO:0042126: nitrate metabolic process (biological_process)
GO:0042126: nitrate metabolic process (biological_process)
GO:0042126: nitrate metabolic process (biological_process)
GO:0042126: nitrate metabolic process (biological_process)
GO:0042126: nitrate metabolic process (biological_process)
GO:0042126: nitrate metabolic process (biological_process)

Components
Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
periplasmic nitrate reductase, large subunitNapAYESTIGR01706 (HMM): periplasmic nitrate reductase, large subunitGO:0042126: nitrate metabolic process
periplasmic nitrate reductase, large subunitNapAYESTIGR01706 (HMM): periplasmic nitrate reductase, large subunitGO:0042126: nitrate metabolic process
periplasmic nitrate reductase, large subunitNapAYESTIGR01706 (HMM): periplasmic nitrate reductase, large subunitGO:0042126: nitrate metabolic process
nitrate reductase cytochrome c-type subunitNapBYESPF03892 (HMM): periplasmic nitrate reductase, diheme cytochrome c subunitGO:0042126: nitrate metabolic process
nitrate reductase cytochrome c-type subunitNapBYESPF03892 (HMM): periplasmic nitrate reductase, diheme cytochrome c subunitGO:0042126: nitrate metabolic process
nitrate reductase cytochrome c-type subunitNapBYESPF03892 (HMM): periplasmic nitrate reductase, diheme cytochrome c subunitGO:0042126: nitrate metabolic process
NapC electron transfer proteinNapCYESTIGR02161 (HMM): periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT familyGO:0042126: nitrate metabolic process
NapC electron transfer proteinNapCYESTIGR02161 (HMM): periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT familyGO:0042126: nitrate metabolic process
NapC electron transfer proteinNapCYESTIGR02161 (HMM): periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT familyGO:0042126: nitrate metabolic process
TAT signal chaperone NapDNapDYESPF03927 (HMM): NapD proteinGO:0042126: nitrate metabolic process
TAT signal chaperone NapDNapDYESPF03927 (HMM): NapD proteinGO:0042126: nitrate metabolic process
TAT signal chaperone NapDNapDYESPF03927 (HMM): NapD proteinGO:0042126: nitrate metabolic process
periplasmic nitrate reductase, NapENapENOTIGR02973 (HMM): periplasmic nitrate reductase, NapE proteinGO:0042126: nitrate metabolic process
periplasmic nitrate reductase, NapENapENOTIGR02973 (HMM): periplasmic nitrate reductase, NapE proteinGO:0042126: nitrate metabolic process
periplasmic nitrate reductase, NapENapENOTIGR02973 (HMM): periplasmic nitrate reductase, NapE proteinGO:0042126: nitrate metabolic process
ferredoxin - type protein NapFNapFNOTIGR00402 (HMM): ferredoxin-type protein NapFGO:0042126: nitrate metabolic process
ferredoxin - type protein NapFNapFNOTIGR00402 (HMM): ferredoxin-type protein NapFGO:0042126: nitrate metabolic process
ferredoxin - type protein NapFNapFNOTIGR00402 (HMM): ferredoxin-type protein NapFGO:0042126: nitrate metabolic process
periplasmic nitrate reductase, NapG subunitNapGNO2263 (RULE_BASE)
GO:0042126: nitrate metabolic process
periplasmic nitrate reductase, NapG subunitNapGNO2263 (RULE_BASE)
GO:0042126: nitrate metabolic process
periplasmic nitrate reductase, NapG subunitNapGNO2263 (RULE_BASE)
GO:0042126: nitrate metabolic process
periplasmic nitrate reductase, NapH subunitNapHNO2262 (RULE_BASE)
GO:0042126: nitrate metabolic process
periplasmic nitrate reductase, NapH subunitNapHNO2262 (RULE_BASE)
GO:0042126: nitrate metabolic process
periplasmic nitrate reductase, NapH subunitNapHNO2262 (RULE_BASE)
GO:0042126: nitrate metabolic process

Parent Properties
AccessionName
GenProp0202nitrogen metabolism
GenProp0202nitrogen metabolism
GenProp0202nitrogen metabolism


Sibling Properties
AccessionName
GenProp0029nitrogen fixation
GenProp0666membrane-associated monooxygenase (methane/ammonia)
GenProp0682formate-dependent nitrite reductase, seven-gene type
GenProp0683cytochrome c nitrite reductase NrfHA
GenProp0814urea utilization
GenProp0899nitrile hydratase