PDBsum entry 1q16

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Oxidoreductase PDB id
Protein chains
1244 a.a. *
509 a.a. *
224 a.a. *
MD1 ×2
SF4 ×4
HEM ×2
Waters ×1213
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of nitrate reductase a, narghi, from escherichia coli
Structure: Respiratory nitrate reductase 1 alpha chain. Chain: a. Engineered: yes. Respiratory nitrate reductase 1 beta chain. Chain: b. Engineered: yes. Respiratory nitrate reductase 1 gamma chain. Chain: c. Synonym: cytochrome b-nr.
Source: Escherichia coli. Organism_taxid: 562. Gene: narg. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: narh. Gene: nari.
Biol. unit: Hexamer (from PQS)
1.90Å     R-factor:   0.202     R-free:   0.230
Authors: M.G.Bertero,N.C.J.Strynadka
Key ref:
M.G.Bertero et al. (2003). Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat Struct Biol, 10, 681-687. PubMed id: 12910261 DOI: 10.1038/nsb969
18-Jul-03     Release date:   07-Oct-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P09152  (NARG_ECOLI) -  Respiratory nitrate reductase 1 alpha chain
1247 a.a.
1244 a.a.
Protein chain
Pfam   ArchSchema ?
P11349  (NARH_ECOLI) -  Respiratory nitrate reductase 1 beta chain
512 a.a.
509 a.a.
Protein chain
Pfam   ArchSchema ?
P11350  (NARI_ECOLI) -  Respiratory nitrate reductase 1 gamma chain
225 a.a.
224 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.  - Nitrate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nitrite + acceptor = nitrate + reduced acceptor
+ acceptor
= nitrate
+ reduced acceptor
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     electron carrier activity     10 terms  


    Added reference    
DOI no: 10.1038/nsb969 Nat Struct Biol 10:681-687 (2003)
PubMed id: 12910261  
Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A.
M.G.Bertero, R.A.Rothery, M.Palak, C.Hou, D.Lim, F.Blasco, J.H.Weiner, N.C.Strynadka.
The facultative anaerobe Escherichia coli is able to assemble specific respiratory chains by synthesis of appropriate dehydrogenases and reductases in response to the availability of specific substrates. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (nitrate reductase A; NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. We present here the crystal structure of NarGHI at a resolution of 1.9 A. The NarGHI structure identifies the number, coordination scheme and environment of the redox-active prosthetic groups, a unique coordination of the molybdenum atom, the first structural evidence for the role of an open bicyclic form of the molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) cofactor in the catalytic mechanism and a novel fold of the membrane anchor subunit. Our findings provide fundamental molecular details for understanding the mechanism of proton-motive force generation by a redox loop.
  Selected figure(s)  
Figure 1.
Figure 1. Proposed mechanism for the proton-motive force generating redox loop by NarGHI and FdnGHI. MQ and MQH2, menoquinone and menaquinol, respectively; b[D] and b[P], distal and proximal heme, respectively; FS, [Fe-S] clusters; Mo-bisMGD, molybdenum cofactor.
Figure 5.
Figure 5. Structure of the integral membrane NarI subunit. (a) Ribbon representation of NarI viewed parallel to the membrane. NarI transmembrane helices are numbered from I to V. Hemes b[P] and b[D] are shown in magenta stick rendering with the Fe atoms in orange. (b) GRASP37 surface representation of NarI viewed from the same direction as in a. Polar and hydrophobic areas are in gray and green, respectively. The region above the dotted line is involved in interactions with NarGH.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 681-687) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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21186382 P.V.Bernhardt (2011).
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Cardiolipin-based respiratory complex activation in bacteria.
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21460452 R.J.Read, and A.J.McCoy (2011).
Using SAD data in Phaser.
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20636266 A.A.Filimonenkov, R.A.Zvyagilskaya, T.V.Tikhonova, and V.O.Popov (2010).
Isolation and characterization of nitrate reductase from the halophilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens.
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Experimental phasing: best practice and pitfalls.
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Crystal structures of all-alpha type membrane proteins.
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20595262 M.Fischer, J.Alderson, G.van Keulen, J.White, and R.G.Sawers (2010).
The obligate aerobe Streptomyces coelicolor A3(2) synthesizes three active respiratory nitrate reductases.
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Direct evidence for nitrogen ligation to the high stability semiquinone intermediate in Escherichia coli nitrate reductase A.
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20204450 S.J.Facey, and A.Kuhn (2010).
Biogenesis of bacterial inner-membrane proteins.
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Basis of recognition between the NarJ chaperone and the N-terminus of the NarG subunit from Escherichia coli nitrate reductase.
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19818162 A.G.Lee (2009).
The effects of lipids on channel function.
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19259562 A.Majumdar, K.Pal, and S.Sarkar (2009).
Necessity of fine tuning in Mo(iv) bis(dithiolene) complexes to warrant nitrate reduction.
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19658738 A.Y.Smirnov, S.E.Savel'ev, and F.Nori (2009).
Diffusion-controlled generation of a proton-motive force across a biomembrane.
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19415239 D.Guymer, J.Maillard, and F.Sargent (2009).
A genetic analysis of in vivo selenate reduction by Salmonella enterica serovar Typhimurium LT2 and Escherichia coli K12.
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19675644 G.Schwarz, R.R.Mendel, and M.W.Ribbe (2009).
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19536822 G.Zoppellaro, K.L.Bren, A.A.Ensign, E.Harbitz, R.Kaur, H.P.Hersleth, U.Ryde, L.Hederstedt, and K.K.Andersson (2009).
Review: studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination.
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19295650 H.Li, and R.J.Turner (2009).
In vivo associations of Escherichia coli NarJ with a peptide of the first 50 residues of nitrate reductase catalytic subunit NarG.
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19241371 K.Conrath, A.S.Pereira, C.E.Martins, C.G.Timóteo, P.Tavares, S.Spinelli, J.Kinne, C.Flaudrops, C.Cambillau, S.Muyldermans, I.Moura, J.J.Moura, M.Tegoni, and A.Desmyter (2009).
Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase.
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19484273 M.Hofmann (2009).
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19452052 M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
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19206188 S.Groysman, and R.H.Holm (2009).
Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites.
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18704520 C.Correia, S.Besson, C.D.Brondino, P.J.González, G.Fauque, J.Lampreia, I.Moura, and J.J.Moura (2008).
Biochemical and spectroscopic characterization of the membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617.
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18635537 C.E.Price, and A.J.Driessen (2008).
YidC Is Involved in the Biogenesis of Anaerobic Respiratory Complexes in the Inner Membrane of Escherichia coli.
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18761683 F.Cava, O.Zafra, and J.Berenguer (2008).
A cytochrome c containing nitrate reductase plays a role in electron transport for denitrification in Thermus thermophilus without involvement of the bc respiratory complex.
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18535145 G.J.Workun, K.Moquin, R.A.Rothery, and J.H.Weiner (2008).
Evolutionary persistence of the molybdopyranopterin-containing sulfite oxidase protein fold.
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18716757 I.Lüke, G.Butland, K.Moore, G.Buchanan, V.Lyall, S.A.Fairhurst, J.F.Greenblatt, A.Emili, T.Palmer, and F.Sargent (2008).
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18719950 I.Moura, S.R.Pauleta, and J.J.Moura (2008).
Enzymatic activity mastered by altering metal coordination spheres.
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18536726 M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, and S.Iwata (2008).
Molecular mechanism of energy conservation in polysulfide respiration.
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PDB codes: 2vpw 2vpx 2vpy 2vpz
18285340 N.J.Gilberthorpe, and R.K.Poole (2008).
Nitric oxide homeostasis in Salmonella typhimurium: roles of respiratory nitrate reductase and flavohemoglobin.
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18607648 N.L.Creevey, A.G.McEwan, and P.V.Bernhardt (2008).
A mechanistic and electrochemical study of the interaction between dimethyl sulfide dehydrogenase and its electron transfer partner cytochrome c (2).
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18522945 O.Genest, M.Neumann, F.Seduk, W.Stöcklein, V.Méjean, S.Leimkühler, and C.Iobbi-Nivol (2008).
Dedicated metallochaperone connects apoenzyme and molybdenum cofactor biosynthesis components.
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18327621 S.Najmudin, P.J.González, J.Trincão, C.Coelho, A.Mukhopadhyay, N.M.Cerqueira, C.C.Romão, I.Moura, J.J.Moura, C.D.Brondino, and M.J.Romão (2008).
Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum.
  J Biol Inorg Chem, 13, 737-753.
PDB codes: 2jim 2jio 2jip 2jiq 2jir 2v3v 2v45
18667702 T.Reda, C.M.Plugge, N.J.Abram, and J.Hirst (2008).
Reversible interconversion of carbon dioxide and formate by an electroactive enzyme.
  Proc Natl Acad Sci U S A, 105, 10654-10658.  
19018282 T.Zhou, P.J.Enyeart, and C.O.Wilke (2008).
Detecting clusters of mutations.
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18501187 W.Liu, C.E.Rogge, G.F.da Silva, V.P.Shinkarev, A.L.Tsai, Y.Kamensky, G.Palmer, and R.J.Kulmacz (2008).
His92 and His110 selectively affect different heme centers of adrenal cytochrome b(561).
  Biochim Biophys Acta, 1777, 1218-1228.  
17130127 B.J.Jepson, S.Mohan, T.A.Clarke, A.J.Gates, J.A.Cole, C.S.Butler, J.N.Butt, A.M.Hemmings, and D.J.Richardson (2007).
Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli.
  J Biol Chem, 282, 6425-6437.
PDB code: 2nya
17360611 G.B.Seiffert, G.M.Ullmann, A.Messerschmidt, B.Schink, P.M.Kroneck, and O.Einsle (2007).
Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase.
  Proc Natl Acad Sci U S A, 104, 3073-3077.
PDB code: 2e7z
17640900 G.Yakovlev, T.Reda, and J.Hirst (2007).
Reevaluating the relationship between EPR spectra and enzyme structure for the iron sulfur clusters in NADH:quinone oxidoreductase.
  Proc Natl Acad Sci U S A, 104, 12720-12725.  
17349816 J.Heider (2007).
Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms.
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17994012 K.A.Vincent, X.Li, C.F.Blanford, N.A.Belsey, J.H.Weiner, and F.A.Armstrong (2007).
Enzymatic catalysis on conducting graphite particles.
  Nat Chem Biol, 3, 761-762.  
17636351 M.Hofmann (2007).
Density functional theory studies of model complexes for molybdenum-dependent nitrate reductase active sites.
  J Biol Inorg Chem, 12, 989.  
17442677 P.Lanciano, A.Vergnes, S.Grimaldi, B.Guigliarelli, and A.Magalon (2007).
Biogenesis of a respiratory complex is orchestrated by a single accessory protein.
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17888006 R.M.Martinez-Espinosa, E.J.Dridge, M.J.Bonete, J.N.Butt, C.S.Butler, F.Sargent, and D.J.Richardson (2007).
Look on the positive side! The orientation, identification and bioenergetics of 'Archaeal' membrane-bound nitrate reductases.
  FEMS Microbiol Lett, 276, 129-139.  
17938909 T.Maeda, V.Sanchez-Torres, and T.K.Wood (2007).
Enhanced hydrogen production from glucose by metabolically engineered Escherichia coli.
  Appl Microbiol Biotechnol, 77, 879-890.  
17471372 X.Ma, C.Schulzke, H.G.Schmidt, and M.Noltemeyer (2007).
Structural, electrochemical and oxygen atom transfer properties of a molybdenum selenoether complex [Mo2O4(OC3H6SeC3H6O)2] and its thioether analogue [Mo2O4(OC3H6SC3H6O)2].
  Dalton Trans, (), 1773-1780.  
16286471 A.Vergnes, J.Pommier, R.Toci, F.Blasco, G.Giordano, and A.Magalon (2006).
NarJ chaperone binds on two distinct sites of the aponitrate reductase of Escherichia coli to coordinate molybdenum cofactor insertion and assembly.
  J Biol Chem, 281, 2170-2176.  
16873117 C.C.Moser, C.C.Page, and P.L.Dutton (2006).
Darwin at the molecular scale: selection and variance in electron tunnelling proteins including cytochrome c oxidase.
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16962969 D.P.Kloer, C.Hagel, J.Heider, and G.E.Schulz (2006).
Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.
  Structure, 14, 1377-1388.
PDB code: 2ivf
16317791 D.W.Heinz, M.S.Weiss, and K.U.Wendt (2006).
Biomacromolecular interactions, assemblies and machines: a structural view.
  Chembiochem, 7, 203-208.  
16829675 E.Maklashina, P.Hellwig, R.A.Rothery, V.Kotlyar, Y.Sher, J.H.Weiner, and G.Cecchini (2006).
Differences in protonation of ubiquinone and menaquinone in fumarate reductase from Escherichia coli.
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17215877 E.O.Oloo, C.Kandt, M.L.O'Mara, and D.P.Tieleman (2006).
Computer simulations of ABC transporter components.
  Biochem Cell Biol, 84, 900-911.  
16885262 H.Ridley, C.A.Watts, D.J.Richardson, and C.S.Butler (2006).
Resolution of distinct membrane-bound enzymes from Enterobacter cloacae SLD1a-1 that are responsible for selective reduction of nitrate and selenate oxyanions.
  Appl Environ Microbiol, 72, 5173-5180.  
16704340 J.F.Stolz, P.Basu, J.M.Santini, and R.S.Oremland (2006).
Arsenic and selenium in microbial metabolism.
  Annu Rev Microbiol, 60, 107-130.  
16873364 K.Fischer, A.Llamas, M.Tejada-Jimenez, N.Schrader, J.Kuper, F.S.Ataya, A.Galvan, R.R.Mendel, E.Fernandez, and G.Schwarz (2006).
Function and structure of the molybdenum cofactor carrier protein from Chlamydomonas reinhardtii.
  J Biol Chem, 281, 30186-30194.
PDB codes: 2iz5 2iz6 2iz7
16469879 L.A.Sazanov, and P.Hinchliffe (2006).
Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus.
  Science, 311, 1430-1436.
PDB code: 2fug
17024183 M.G.Madej, H.R.Nasiri, N.S.Hilgendorff, H.Schwalbe, and C.R.Lancaster (2006).
Evidence for transmembrane proton transfer in a dihaem-containing membrane protein complex.
  EMBO J, 25, 4963-4970.
PDB code: 2bs2
16864586 S.M.Southall, J.J.Doel, D.J.Richardson, and A.Oubrie (2006).
Soluble aldose sugar dehydrogenase from Escherichia coli: a highly exposed active site conferring broad substrate specificity.
  J Biol Chem, 281, 30650-30659.
PDB code: 2g8s
16864590 V.W.Cheng, E.Ma, Z.Zhao, R.A.Rothery, and J.H.Weiner (2006).
The iron-sulfur clusters in Escherichia coli succinate dehydrogenase direct electron flow.
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16172928 A.J.Watson, A.V.Hughes, P.K.Fyfe, M.C.Wakeham, K.Holden-Dye, P.Heathcote, and M.R.Jones (2005).
On the role of basic residues in adapting the reaction centre-LH1 complex for growth at elevated temperatures in purple bacteria.
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16234939 A.Thapper, A.Behrens, J.Fryxelius, M.H.Johansson, F.Prestopino, M.Czaun, D.Rehder, and E.Nordlander (2005).
Synthesis and characterization of molybdenum oxo complexes of two tripodal ligands: reactivity studies of a functional model for molybdenum oxotransferases.
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16380425 C.R.Lancaster, U.S.Sauer, R.Gross, A.H.Haas, J.Graf, H.Schwalbe, W.Mäntele, J.Simon, and M.G.Madej (2005).
Experimental support for the "E pathway hypothesis" of coupled transmembrane e- and H+ transfer in dihemic quinol:fumarate reductase.
  Proc Natl Acad Sci U S A, 102, 18860-18865.
PDB codes: 2bs3 2bs4
15716436 J.A.Müller, and S.DasSarma (2005).
Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors.
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16234940 J.P.McNamara, I.H.Hillier, T.S.Bhachu, and C.D.Garner (2005).
The nature and function of the catalytic centres of the DMSO reductases.
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15615728 M.G.Bertero, R.A.Rothery, N.Boroumand, M.Palak, F.Blasco, N.Ginet, J.H.Weiner, and N.C.Strynadka (2005).
Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A.
  J Biol Chem, 280, 14836-14843.
PDB codes: 1y4z 1y5i 1y5l 1y5n
16236714 M.Guiral, P.Tron, C.Aubert, A.Gloter, C.Iobbi-Nivol, and M.T.Giudici-Orticoni (2005).
A membrane-bound multienzyme, hydrogen-oxidizing, and sulfur-reducing complex from the hyperthermophilic bacterium Aquifex aeolicus.
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15937161 O.Zafra, F.Cava, F.Blasco, A.Magalon, and J.Berenguer (2005).
Membrane-associated maturation of the heterotetrameric nitrate reductase of Thermus thermophilus.
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15654871 R.A.Rothery, A.M.Seime, A.M.Spiers, E.Maklashina, I.Schröder, R.P.Gunsalus, G.Cecchini, and J.H.Weiner (2005).
Defining the Q-site of Escherichia coli fumarate reductase by site-directed mutagenesis, fluorescence quench titrations and EPR spectroscopy.
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16234941 S.J.Field, N.P.Thornton, L.J.Anderson, A.J.Gates, A.Reilly, B.J.Jepson, D.J.Richardson, S.J.George, M.R.Cheesman, and J.N.Butt (2005).
Reductive activation of nitrate reductases.
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15247236 A.Vergnes, K.Gouffi-Belhabich, F.Blasco, G.Giordano, and A.Magalon (2004).
Involvement of the molybdenum cofactor biosynthetic machinery in the maturation of the Escherichia coli nitrate reductase A.
  J Biol Chem, 279, 41398-41403.  
15166246 B.J.Jepson, L.J.Anderson, L.M.Rubio, C.J.Taylor, C.S.Butler, E.Flores, A.Herrero, J.N.Butt, and D.J.Richardson (2004).
Tuning a nitrate reductase for function. The first spectropotentiometric characterization of a bacterial assimilatory nitrate reductase reveals novel redox properties.
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15311335 J.J.Moura, C.D.Brondino, J.Trincão, and M.J.Romão (2004).
Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases.
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15306815 J.Kuper, A.Llamas, H.J.Hecht, R.R.Mendel, and G.Schwarz (2004).
Structure of the molybdopterin-bound Cnx1G domain links molybdenum and copper metabolism.
  Nature, 430, 803-806.
PDB codes: 1uux 1uuy
15355966 L.Loschi, S.J.Brokx, T.L.Hills, G.Zhang, M.G.Bertero, A.L.Lovering, J.H.Weiner, and N.C.Strynadka (2004).
Structural and biochemical identification of a novel bacterial oxidoreductase.
  J Biol Chem, 279, 50391-50400.
PDB codes: 1xdq 1xdy
15551861 O.Einsle, and P.M.Kroneck (2004).
Structural basis of denitrification.
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15182355 R.Giordani, and J.Buc (2004).
Evidence for two different electron transfer pathways in the same enzyme, nitrate reductase A from Escherichia coli.
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14576151 R.Gross, R.Pisa, M.Sänger, C.R.Lancaster, and J.Simon (2004).
Characterization of the menaquinone reduction site in the diheme cytochrome b membrane anchor of Wolinella succinogenes NiFe-hydrogenase.
  J Biol Chem, 279, 274-281.  
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