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PDBsum entry 1nid

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Oxidoreductase (nitric oxide(a)) PDB id
1nid
Jmol
Contents
Protein chain
333 a.a. *
Ligands
NO2
Metals
_CU ×2
Waters ×172
* Residue conservation analysis
PDB id:
1nid
Name: Oxidoreductase (nitric oxide(a))
Title: The structure of cu-nitrite reductase from achromobacter cyc at five ph values, with nitrite bound and with type ii cu d
Structure: Nitrite reductase. Chain: a. Other_details: ph 5.4 ("nt1") nitrite soaked
Source: Achromobacter cycloclastes. Organism_taxid: 223
Biol. unit: Trimer (from PQS)
Resolution:
2.20Å     R-factor:   0.149    
Authors: E.T.Adman,J.W.Godden,S.Turley
Key ref: E.T.Adman et al. (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, 27458-27474. PubMed id: 7499203
Date:
03-Jul-95     Release date:   07-Dec-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P25006  (NIR_ACHCY) -  Copper-containing nitrite reductase
Seq:
Struc:
378 a.a.
333 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: Cu cation or Fe cation; FAD
Cu cation
or Fe cation
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   4 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
J Biol Chem 270:27458-27474 (1995)
PubMed id: 7499203  
 
 
The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted.
E.T.Adman, J.W.Godden, S.Turley.
 
  ABSTRACT  
 
High resolution x-ray crystallographic structures of nitrite reductase from Achromobacter cycloclastes, undertaken in order to understand the pH optimum of the reaction with nitrite, show that at pH 5.0, 5.4, 6.0, 6.2, and 6.8, no significant changes occur, other than in the occupancy of the type II copper at the active site. An extensive network of hydrogen bonds, both within and between subunits of the trimer, maintains the rigidity of the protein structure. A water occupies a site approximately 1.5 A from the site of the type II copper in the structure of the type II copper-depleted structure (at pH 5.4), again with no other significant changes in structure. In nitrite-soaked crystals, nitrite binds via its oxygens to the type II copper and replaces the water normally bound to the type II copper. The active-site cavity of the protein is distinctly hydrophobic on one side and hydrophilic on the other, providing a possible path for diffusion of the product NO. Asp-98 exhibits thermal parameter values higher than its surroundings, suggesting a role in shuttling the two protons necessary for the overall reaction. The strong structural homology with cupredoxins is described.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20083495 I.S.MacPherson, F.I.Rosell, M.Scofield, A.G.Mauk, and M.E.Murphy (2010).
Directed evolution of copper nitrite reductase to a chromogenic reductant.
  Protein Eng Des Sel, 23, 137-145.
PDB codes: 3h4f 3h4h 3h56
19701722 M.B.Rajasekaran, S.Nilapwar, S.C.Andrews, and K.A.Watson (2010).
EfeO-cupredoxins: major new members of the cupredoxin superfamily with roles in bacterial iron transport.
  Biometals, 23, 1.  
20056148 M.Rusu, and S.Birmanns (2010).
Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.
  J Struct Biol, 170, 164-171.  
  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.  
19586913 S.Brenner, D.J.Heyes, S.Hay, M.A.Hough, R.R.Eady, S.S.Hasnain, and N.S.Scrutton (2009).
Demonstration of proton-coupled electron transfer in the copper-containing nitrite reductases.
  J Biol Chem, 284, 25973-25983.  
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.  
19282479 S.Ghosh, X.Xie, A.Dey, Y.Sun, C.P.Scholes, and E.I.Solomon (2009).
Thermodynamic equilibrium between blue and green copper sites and the role of the protein in controlling function.
  Proc Natl Acad Sci U S A, 106, 4969-4974.  
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
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.  
18708469 T.Kawabata (2008).
Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model.
  Biophys J, 95, 4643-4658.  
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.  
16795108 K.Sato, and C.Dennison (2006).
Active site comparison of CoII blue and green nitrite reductases.
  Chemistry, 12, 6647-6659.  
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
15182351 D.Pinho, S.Besson, C.D.Brondino, B.de Castro, and I.Moura (2004).
Copper-containing nitrite reductase from Pseudomonas chlororaphis DSM 50135.
  Eur J Biochem, 271, 2361-2369.  
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
11916709 A.Priemé, G.Braker, and J.M.Tiedje (2002).
Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils.
  Appl Environ Microbiol, 68, 1893-1900.  
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.  
12039012 R.K.Szilagyi, and E.I.Solomon (2002).
Electronic structure and its relation to function in copper proteins.
  Curr Opin Chem Biol, 6, 250-258.  
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.  
11282344 I.Moura, and J.J.Moura (2001).
Structural aspects of denitrifying enzymes.
  Curr Opin Chem Biol, 5, 168-175.  
11319103 K.L.Casciotti, and B.B.Ward (2001).
Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria.
  Appl Environ Microbiol, 67, 2213-2221.  
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.  
10398364 J.O.De Kerpel, and U.Ryde (1999).
Protein strain in blue copper proteins studied by free energy perturbations.
  Proteins, 36, 157-174.  
10223295 M.H.Seto, H.L.Liu, D.A.Zajchowski, and M.Whitlow (1999).
Protein fold analysis of the B30.2-like domain.
  Proteins, 35, 235-249.  
  10197991 M.Prudêncio, R.R.Eady, and G.Sawers (1999).
The blue copper-containing nitrite reductase from Alcaligenes xylosoxidans: cloning of the nirA gene and characterization of the recombinant enzyme.
  J Bacteriol, 181, 2323-2329.  
9520385 A.Messerschmidt, L.Prade, S.J.Kroes, J.Sanders-Loehr, R.Huber, and G.W.Canters (1998).
Rack-induced metal binding vs. flexibility: Met121His azurin crystal structures at different pH.
  Proc Natl Acad Sci U S A, 95, 3443-3448.
PDB codes: 1a4a 1a4b 1a4c
9558348 A.Veselov, K.Olesen, A.Sienkiewicz, J.P.Shapleigh, and C.P.Scholes (1998).
Electronic structural information from Q-band ENDOR on the type 1 and type 2 copper liganding environment in wild-type and mutant forms of copper-containing nitrite reductase.
  Biochemistry, 37, 6095-6105.  
9558347 K.Olesen, A.Veselov, Y.Zhao, Y.Wang, B.Danner, C.P.Scholes, and J.P.Shapleigh (1998).
Spectroscopic, kinetic, and electrochemical characterization of heterologously expressed wild-type and mutant forms of copper-containing nitrite reductase from Rhodobacter sphaeroides 2.4.3.
  Biochemistry, 37, 6086-6094.  
9315849 B.R.Crane, L.M.Siegel, and E.D.Getzoff (1997).
Probing the catalytic mechanism of sulfite reductase by X-ray crystallography: structures of the Escherichia coli hemoprotein in complex with substrates, inhibitors, intermediates, and products.
  Biochemistry, 36, 12120-12137.
PDB codes: 2gep 3geo 4gep 5gep 6gep 7gep 8gep
9354630 K.Kobayashi, A.Koppenhöfer, S.J.Ferguson, and S.Tagawa (1997).
Pulse radiolysis studies on cytochrome cd1 nitrite reductase from Thiosphaera pantotropha: evidence for a fast intramolecular electron transfer from c-heme to d1-heme.
  Biochemistry, 36, 13611-13616.  
  9098885 M.E.Murphy, P.F.Lindley, and E.T.Adman (1997).
Structural comparison of cupredoxin domains: domain recycling to construct proteins with novel functions.
  Protein Sci, 6, 761-770.  
  9409151 W.G.Zumft (1997).
Cell biology and molecular basis of denitrification.
  Microbiol Mol Biol Rev, 61, 533-616.  
8994881 A.Volbeda, J.C.Fontecilla-Camps, and M.Frey (1996).
Novel metal sites in protein structures.
  Curr Opin Struct Biol, 6, 804-812.  
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 codes are shown on the right.