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Oxidoreductase PDB id
1as6
Jmol
Contents
Protein chains
335 a.a. *
Ligands
NO2 ×3
Metals
_CU ×6
Waters ×2382
* Residue conservation analysis
PDB id:
1as6
Name: Oxidoreductase
Title: Structure of nitrite bound to oxidized alcaligenes faecalis nitrite reductase at cryo temperature
Structure: Nitrite reductase. Chain: a, b, c. Engineered: yes
Source: Alcaligenes faecalis. Organism_taxid: 511. Strain: s-6. Cellular_location: periplasm. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Trimer (from PDB file)
Resolution:
1.80Å     R-factor:   0.181    
Authors: M.E.P.Murphy,E.T.Adman,S.Turley
Key ref:
M.E.Murphy et al. (1997). Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications. J Biol Chem, 272, 28455-28460. PubMed id: 9353305 DOI: 10.1074/jbc.272.45.28455
Date:
13-Aug-97     Release date:   25-Feb-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P38501  (NIR_ALCFA) -  Copper-containing nitrite reductase
Seq:
Struc: 		376 a.a.
335 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.7.2.1  - Nitrite reductase (NO-forming).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+
Nitric oxide
 + H(2)O
 + ferricytochrome c
 =
nitrite
Bound ligand (Het Group name = NO2)
corresponds exactly 		+ ferrocytochrome c
 + 2 × H(+)
      Cofactor: Copper or iron; FAD
Copper
 or iron
 FAD
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     nitrogen compound metabolic process   3 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.272.45.28455 J Biol Chem 272:28455-28460 (1997)
PubMed id: 9353305  
 
 
Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.
M.E.Murphy, S.Turley, E.T.Adman.
 
  ABSTRACT  
 
The structures of oxidized, reduced, nitrite-soaked oxidized and nitrite-soaked reduced nitrite reductase from Alcaligenes faecalis have been determined at 1.8-2.0 A resolution using data collected at -160 degrees C. The active site at cryogenic temperature, as at room temperature, contains a tetrahedral type II copper site liganded by three histidines and a water molecule. The solvent site is empty when crystals are reduced with ascorbate. A fully occupied oxygen-coordinate nitrite occupies the solvent site in crystals soaked in nitrite. Ascorbate-reduced crystals soaked in a glycerol-methanol solution and nitrite at -40 degrees C remain colorless at -160 degrees C but turn amber-brown when warmed, suggesting that NO is released. Nitrite is found at one-half occupancy. Five new solvent sites in the oxidized nitrite bound form exhibit defined but different occupancies in the other three forms. These results support a previously proposed mechanism by which nitrite is bound primarily by a single oxygen atom that is protonable, and after reduction and cleavage of that N-O bond, NO is released leaving the oxygen atom bound to the Cu site as hydroxide or water.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Active sites of oxidized (A), reduced (B), nitrite-soaked (C), and reduced nitrite-soaked (D) NIR. The three histidine^ type II copper ligands and active residues Asp-98, His-255, and^ Ile-257 are drawn as balls and sticks. The active site water, copper atom, and the water molecule bridging Asp-98 and His-255^ are represented by large spheres. Active site water or nitrite^ omit difference (F[o]-F[c]) maps are contoured at 4 . Figure was created using Molscript (31) and Minimage (32). 		Figure 3.
Fig. 3. A proposed mechanism for copper-containing nitrite reductase. The native enzyme (middle left) is represented with a^ hydroxyl ion bound to the active site copper and Asp-98 is protonated. Nitrite displaces the hydroxyl (top right), followed by reduction of the copper (bottom right). Nitrite decomposes after reduction and protonation to give an intermediate with hydroxyl and NO transiently bound to the copper. The native enzyme is restored when NO leaves. NO may rebind to copper, displacing hydroxyl (top left) as a possible^ first step in the production of N[2]O.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 28455-28460) copyright 1997.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20945335 R.Gessmann, C.Kyvelidou, M.Papadovasilaki, and K.Petratos (2011).
The crystal structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis.
  Biopolymers, 95, 202-207.
PDB code: 3nyk
21153850 S.M.Berry, E.L.Bladholm, E.J.Mostad, and A.R.Schenewerk (2011).
Incorporation of the red copper nitrosocyanin binding loop into blue copper azurin.
  J Biol Inorg Chem, 16, 473-480.  
20424749 C.S.Chen, and W.Y.Yeh (2010).
Coordination of NO(2)(-) ligand to Cu(I) ion in an O,O-bidentate fashion that evolves NO gas upon protonation: a model reaction relevant to the denitrification process.
  Chem Commun (Camb), 46, 3098-3100.  
20372697 J.A.Worrall, and E.Vijgenboom (2010).
Copper mining in Streptomyces: enzymes, natural products and development.
  Nat Prod Rep, 27, 742-756.  
  19193999 D.Hira, M.Nojiri, and S.Suzuki (2009).
Crystallization and preliminary X-ray diffraction analysis of a complex between the electron-transfer partners hexameric Cu-containing nitrite reductase and pseudoazurin.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 116-119.  
  19194001 M.Nojiri, F.Shirota, D.Hira, and S.Suzuki (2009).
Expression, purification, crystallization and preliminary X-ray diffraction analysis of the soluble domain of PPA0092, a putative nitrite reductase from Propionibacterium acnes.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 123-127.  
19053185 S.Ghosh, A.Dey, Y.Sun, C.P.Scholes, and E.I.Solomon (2009).
Spectroscopic and computational studies of nitrite reductase: proton induced electron transfer and backbonding contributions to reactivity.
  J Am Chem Soc, 131, 277-288.  
18830721 S.M.Berry, J.R.Mayers, and N.A.Zehm (2009).
Models of noncoupled dinuclear copper centers in azurin.
  J Biol Inorg Chem, 14, 143-149.  
19224923 T.J.Lawton, L.A.Sayavedra-Soto, D.J.Arp, and A.C.Rosenzweig (2009).
Crystal structure of a two-domain multicopper oxidase: implications for the evolution of multicopper blue proteins.
  J Biol Chem, 284, 10174-10180.
PDB code: 3g5w
18030462 G.K.Kong, L.A.Miles, G.A.Crespi, C.J.Morton, H.L.Ng, K.J.Barnham, W.J.McKinstry, R.Cappai, and M.W.Parker (2008).
Copper binding to the Alzheimer's disease amyloid precursor protein.
  Eur Biophys J, 37, 269-279.  
18719950 I.Moura, S.R.Pauleta, and J.J.Moura (2008).
Enzymatic activity mastered by altering metal coordination spheres.
  J Biol Inorg Chem, 13, 1185-1195.  
18303118 S.Kuznetsova, G.Zauner, T.J.Aartsma, H.Engelkamp, N.Hatzakis, A.E.Rowan, R.J.Nolte, P.C.Christianen, and G.W.Canters (2008).
The enzyme mechanism of nitrite reductase studied at single-molecule level.
  Proc Natl Acad Sci U S A, 105, 3250-3255.  
17701241 A.Stirpe, L.Sportelli, H.Wijma, M.P.Verbeet, and R.Guzzi (2007).
Thermal stability effects of removing the type-2 copper ligand His306 at the interface of nitrite reductase subunits.
  Eur Biophys J, 36, 805-813.  
17360521 M.Nojiri, Y.Xie, T.Inoue, T.Yamamoto, H.Matsumura, K.Kataoka, Deligeer, K.Yamaguchi, Y.Kai, and S.Suzuki (2007).
Structure and function of a hexameric copper-containing nitrite reductase.
  Proc Natl Acad Sci U S A, 104, 4315-4320.
PDB code: 2dv6
17186474 S.A.De Marothy, M.R.Blomberg, and P.E.Siegbahn (2007).
Elucidating the mechanism for the reduction of nitrite by copper nitrite reductase--a contribution from quantum chemical studies.
  J Comput Chem, 28, 528-539.  
17685522 S.Ghosh, A.Dey, O.M.Usov, Y.Sun, V.M.Grigoryants, C.P.Scholes, and E.I.Solomon (2007).
Resolution of the spectroscopy versus crystallography issue for NO intermediates of nitrite reductase from Rhodobacter sphaeroides.
  J Am Chem Soc, 129, 10310-10311.  
16568189 A.K.Nairn, S.J.Archibald, R.Bhalla, C.J.Boxwell, A.C.Whitwood, and P.H.Walton (2006).
Syntheses of copper(I)cis-1,3,5-tri-iminocyclohexane complexes.
  Dalton Trans, 0, 1790-1795.  
16389611 M.Kujime, and H.Fujii (2006).
Spectroscopic characterization of reaction intermediates in a model for copper nitrite reductase.
  Angew Chem Int Ed Engl, 45, 1089-1092.  
16447049 W.B.Tolman (2006).
Using synthetic chemistry to understand copper protein active sites: a personal perspective.
  J Biol Inorg Chem, 11, 261-271.  
16138306 A.Impagliazzo, L.Krippahl, and M.Ubbink (2005).
Pseudoazurin-nitrite reductase interactions.
  Chembiochem, 6, 1648-1653.  
16131751 F.Jacobson, H.Guo, K.Olesen, M.Okvist, R.Neutze, and L.Sjölin (2005).
Structures of the oxidized and reduced forms of nitrite reductase from Rhodobacter sphaeroides 2.4.3 at high pH: changes in the interactions of the type 2 copper.
  Acta Crystallogr D Biol Crystallogr, 61, 1190-1198.
PDB codes: 1zv2 2a3t
16093314 S.V.Antonyuk, R.W.Strange, G.Sawers, R.R.Eady, and S.S.Hasnain (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, 12041-12046.
PDB codes: 2bw4 2bw5 2bwd 2bwi
15131298 N.W.Aboelella, A.M.Reynolds, and W.B.Tolman (2004).
Biophysics. Catching copper in the act.
  Science, 304, 836-837.
PDB code: 1snr
15583395 Y.Xie, T.Inoue, N.Seike, H.Matsumura, K.Kanbayashi, K.Itoh, K.Kataoka, K.Yamaguchi, S.Suzuki, and Y.Kai (2004).
Crystallization and preliminary X-ray crystallographic studies of dissimilatory nitrite reductase isolated from Hyphomicrobium denitrificans A3151.
  Acta Crystallogr D Biol Crystallogr, 60, 2383-2386.  
12538888 M.J.Boulanger, and M.E.Murphy (2003).
Directing the mode of nitrite binding to a copper-containing nitrite reductase from Alcaligenes faecalis S-6: characterization of an active site isoleucine.
  Protein Sci, 12, 248-256.
PDB codes: 1l9o 1l9p 1l9q 1l9r 1l9s 1l9t
12777802 O.V.Moroz, A.A.Antson, S.J.Grist, N.J.Maitland, G.G.Dodson, K.S.Wilson, E.Lukanidin, and I.B.Bronstein (2003).
Structure of the human S100A12-copper complex: implications for host-parasite defence.
  Acta Crystallogr D Biol Crystallogr, 59, 859-867.
PDB code: 1odb
11876652 M.Prudêncio, G.Sawers, S.A.Fairhurst, F.K.Yousafzai, and R.R.Eady (2002).
Alcaligenes xylosoxidans dissimilatory nitrite reductase: alanine substitution of the surface-exposed histidine 139l ligand of the type 1 copper center prevents electron transfer to the catalytic center.
  Biochemistry, 41, 3430-3438.  
11867755 S.A.Roberts, A.Weichsel, G.Grass, K.Thakali, J.T.Hazzard, G.Tollin, C.Rensing, and W.R.Montfort (2002).
Crystal structure and electron transfer kinetics of CueO, a multicopper oxidase required for copper homeostasis in Escherichia coli.
  Proc Natl Acad Sci U S A, 99, 2766-2771.
PDB code: 1kv7
12044180 Y.Zhao, D.A.Lukoyanov, Y.V.Toropov, K.Wu, J.P.Shapleigh, and C.P.Scholes (2002).
Catalytic function and local proton structure at the type 2 copper of nitrite reductase: the correlation of enzymatic pH dependence, conserved residues, and proton hyperfine structure.
  Biochemistry, 41, 7464-7474.  
11418554 H.Ichiki, Y.Tanaka, K.Mochizuki, K.Yoshimatsu, T.Sakurai, and T.Fujiwara (2001).
Purification, characterization, and genetic analysis of Cu-containing dissimilatory nitrite reductase from a denitrifying halophilic archaeon, Haloarcula marismortui.
  J Bacteriol, 183, 4149-4156.  
  11282344 I.Moura, and J.J.Moura (2001).
Structural aspects of denitrifying enzymes.
  Curr Opin Chem Biol, 5, 168-175.  
11478880 M.J.Boulanger, and M.E.Murphy (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, 9132-9141.
PDB codes: 1j9q 1j9r 1j9s 1j9t
11468394 M.J.Ellis, F.E.Dodd, R.W.Strange, M.Prudêncio, G.Sawers, R.R.Eady, and S.S.Hasnain (2001).
X-ray structure of a blue copper nitrite reductase at high pH and in copper-free form at 1.9 A resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 1110-1118.
PDB codes: 1hau 1haw
10320660 F.Cutruzzolà (1999).
Bacterial nitric oxide synthesis.
  Biochim Biophys Acta, 1411, 231-249.  
  9667932 S.J.Ferguson (1998).
Nitrogen cycle enzymology.
  Curr Opin Chem Biol, 2, 182-193.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.