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PDBsum entry 1nir

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protein ligands metals Protein-protein interface(s) links
Nitrite reductase PDB id
1nir
Jmol
Contents
Protein chains
538 a.a. *
Ligands
PO4 ×2
_OH ×2
HEC ×2
DHE ×2
Metals
_CL ×2
Waters ×870
* Residue conservation analysis
PDB id:
1nir
Name: Nitrite reductase
Title: Oxydized nitrite reductase from pseudomonas aeruginosa
Structure: Nitrite reductase. Chain: a, b. Other_details: each sub-unit (a, b) linking one phosphate ion and one chloride ion
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Cellular_location: periplasmic space. Other_details: nctc 6750
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.15Å     R-factor:   0.209     R-free:   0.242
Authors: D.Nurizzo,M.Tegoni,C.Cambillau
Key ref:
D.Nurizzo et al. (1997). N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa. Structure, 5, 1157-1171. PubMed id: 9331415 DOI: 10.1016/S0969-2126(97)00267-0
Date:
17-Jun-97     Release date:   03-Dec-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P24474  (NIRS_PSEAE) -  Nitrite reductase
Seq:
Struc:
 
Seq:
Struc:
568 a.a.
539 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: 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
Bound ligand (Het Group name = HEC)
matches with 63.00% similarity
= nitrite
+ ferrocytochrome c
+ 2 × H(+)
      Cofactor: Cu cation or Fe cation; FAD
Cu cation
or Fe cation
FAD
   Enzyme class 3: E.C.1.7.99.1  - Hydroxylamine reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NH3 + H2O + acceptor = hydroxylamine + reduced acceptor
NH(3)
+ H(2)O
+ acceptor
= hydroxylamine
+ reduced acceptor
      Cofactor: Flavoprotein
Iron-sulfur
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
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     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(97)00267-0 Structure 5:1157-1171 (1997)
PubMed id: 9331415  
 
 
N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa.
D.Nurizzo, M.C.Silvestrini, M.Mathieu, F.Cutruzzolà, D.Bourgeois, V.Fülöp, J.Hajdu, M.Brunori, M.Tegoni, C.Cambillau.
 
  ABSTRACT  
 
BACKGROUND: Nitrite reductase from Pseudomonas aeruginosa (NiR-Pa) is a dimer consisting of two identical 60 kDa subunits, each of which contains one c and one d1 heme group. This enzyme, a soluble component of the electron-transfer chain that uses nitrate as a source of energy, can be induced by the addition of nitrate to the bacterial growth medium. NiR-Pa catalyzes the reduction of nitrite (NO2-) to nitric oxide (NO); in vitro, both cytochrome c551 and azurin are efficient electron donors in this reaction. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. RESULTS: The structure of the orthorhombic form (P2(1)2(1)2) of oxidized NiR-Pa was solved at 2.15 A resolution, using molecular replacement with the coordinates of the NiR from Thiosphaera pantotropha (NiR-Tp) as the starting model. Although the d1-heme domains are almost identical in both enzyme structures, the c domain of NiR-Pa is more like the classical class I cytochrome-c fold because it has His51 and Met88 as heme ligands, instead of His17 and His69 present in NiR-Tp. In addition, the methionine-bearing loop, which was displaced by His17 of the NiR-Tp N-terminal segment, is back to normal in our structure. The N-terminal residues (5/6-30) of NiR-Pa and NiR-Tp have little sequence identity. In Nir-Pa, this N-terminal segment of one monomer crosses the dimer interface and wraps itself around the other monomer. Tyr10 of this segment is hydrogen bonded to an hydroxide ion--the sixth ligand of the d1-heme Fe, whereas the equivalent residue in NiR-Tp, Tyr25, is directly bound to the Fe. CONCLUSIONS: Two ligands of hemes c and d1 differ between the two known NiR structures, which accounts for the fact that they have quite different spectroscopic and kinetic features. The unexpected domain-crossing by the N-terminal segment of NiR-Pa is comparable to that of 'domain swapping' or 'arm exchange' previously observed in other systems and may explain the observed cooperativity between monomers of dimeric NiR-Pa. In spite of having similar sequence and fold, the different kinetic behaviour and the spectral features of NiR-Pa and NiR-Tp are tuned by the N-terminal stretch of residues. A further example of this may come from another NiR, from Pseudomonas stutzeri, which has an N terminus very different from that of the two above mentioned NiRs.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Water-accessible surface area of NiR-Pa monomer A, slabbed at the level of the d[1] heme. Water molecules are colored in blue, the d[1] heme in red and the phosphate ion in green. The channel starting from the d[1] heme and leading to the `back door' is located between the d[1] heme and the phosphate ion.
 
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1157-1171) copyright 1997.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265772 S.Rinaldo, G.Giardina, N.Castiglione, V.Stelitano, and F.Cutruzzolà (2011).
The catalytic mechanism of Pseudomonas aeruginosa cd1 nitrite reductase.
  Biochem Soc Trans, 39, 195-200.  
19554608 F.Cutruzzolà, S.Rinaldo, N.Castiglione, G.Giardina, I.Pecht, and M.Brunori (2009).
Nitrite reduction: a ubiquitous function from a pre-aerobic past.
  Bioessays, 31, 885-891.  
19348767 O.Farver, M.Brunori, F.Cutruzzolà, S.Rinaldo, S.Wherland, and I.Pecht (2009).
Intramolecular electron transfer in Pseudomonas aeruginosa cd(1) nitrite reductase: thermodynamics and kinetics.
  Biophys J, 96, 2849-2856.  
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.  
17148448 F.Jacobson, A.Pistorius, D.Farkas, W.De Grip, O.Hansson, L.Sjölin, and R.Neutze (2007).
pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase.
  J Biol Chem, 282, 6347-6355.
PDB codes: 2dws 2dwt 2dy2
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
15901734 R.S.Zajicek, M.R.Cheesman, E.H.Gordon, and S.J.Ferguson (2005).
Y25S variant of Paracoccus pantotrophus cytochrome cd1 provides insight into anion binding by d1 heme and a rare example of a critical difference between solution and crystal structures.
  J Biol Chem, 280, 26073-26079.  
15551861 O.Einsle, and P.M.Kroneck (2004).
Structural basis of denitrification.
  Biol Chem, 385, 875-883.  
12556530 E.H.Gordon, T.Sjögren, M.Löfqvist, C.D.Richter, J.W.Allen, C.W.Higham, J.Hajdu, V.Fülöp, and S.J.Ferguson (2003).
Structure and kinetic properties of Paracoccus pantotrophus cytochrome cd1 nitrite reductase with the d1 heme active site ligand tyrosine 25 replaced by serine.
  J Biol Chem, 278, 11773-11781.
PDB code: 1gq1
11709555 C.D.Richter, J.W.Allen, C.W.Higham, A.Koppenhofer, R.S.Zajicek, N.J.Watmough, and S.J.Ferguson (2002).
Cytochrome cd1, reductive activation and kinetic analysis of a multifunctional respiratory enzyme.
  J Biol Chem, 277, 3093-3100.  
11226222 F.Cutruzzola, K.Brown, E.K.Wilson, A.Bellelli, M.Arese, M.Tegoni, C.Cambillau, and M.Brunori (2001).
The nitrite reductase from Pseudomonas aeruginosa: essential role of two active-site histidines in the catalytic and structural properties.
  Proc Natl Acad Sci U S A, 98, 2232-2237.  
11282344 I.Moura, and J.J.Moura (2001).
Structural aspects of denitrifying enzymes.
  Curr Opin Chem Biol, 5, 168-175.  
11456493 K.Kobayashi, A.Koppenhöfer, S.J.Ferguson, N.J.Watmough, and S.Tagawa (2001).
Intramolecular electron transfer from c heme to d1 heme in bacterial cytochrome cd1 nitrite reductase occurs over the same distances at very different rates depending on the source of the enzyme.
  Biochemistry, 40, 8542-8547.  
10757972 A.Koppenhöfer, K.L.Turner, J.W.Allen, S.K.Chapman, and S.J.Ferguson (2000).
Cytochrome cd(1) from Paracoccus pantotrophus exhibits kinetically gated, conformationally dependent, highly cooperative two-electron redox behavior.
  Biochemistry, 39, 4243-4249.  
10747791 A.Koppenhöfer, R.H.Little, D.J.Lowe, S.J.Ferguson, and N.J.Watmough (2000).
Oxidase reaction of cytochrome cd(1) from Paracoccus pantotrophus.
  Biochemistry, 39, 4028-4036.  
10940005 C.G.Friedrich, A.Quentmeier, F.Bardischewsky, D.Rother, R.Kraft, S.Kostka, and H.Prinz (2000).
Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17.
  J Bacteriol, 182, 4677-4687.  
10998232 G.Ranghino, E.Scorza, T.Sjögren, P.A.Williams, M.Ricci, and J.Hajdu (2000).
Quantum mechanical interpretation of nitrite reduction by cytochrome cd1 nitrite reductase from Paracoccus pantotrophus.
  Biochemistry, 39, 10958-10966.  
10998233 T.Sjögren, M.Svensson-Ek, J.Hajdu, and P.Brzezinski (2000).
Proton-coupled structural changes upon binding of carbon monoxide to cytochrome cd1: a combined flash photolysis and X-ray crystallography study.
  Biochemistry, 39, 10967-10974.
PDB code: 1dy7
10562539 B.R.Crane, R.J.Rosenfeld, A.S.Arvai, D.K.Ghosh, S.Ghosh, J.A.Tainer, D.J.Stuehr, and E.D.Getzoff (1999).
N-terminal domain swapping and metal ion binding in nitric oxide synthase dimerization.
  EMBO J, 18, 6271-6281.
PDB codes: 1df1 1qom
10348621 D.J.Richardson, and N.J.Watmough (1999).
Inorganic nitrogen metabolism in bacteria.
  Curr Opin Chem Biol, 3, 207-219.  
10562538 D.K.Ghosh, B.R.Crane, S.Ghosh, D.Wolan, R.Gachhui, C.Crooks, A.Presta, J.A.Tainer, E.D.Getzoff, and D.J.Stuehr (1999).
Inducible nitric oxide synthase: role of the N-terminal beta-hairpin hook and pterin-binding segment in dimerization and tetrahydrobiopterin interaction.
  EMBO J, 18, 6260-6270.
PDB codes: 1dwv 1dww 1dwx
10329702 D.Nurizzo, F.Cutruzzolà, M.Arese, D.Bourgeois, M.Brunori, C.Cambillau, and M.Tegoni (1999).
Does the reduction of c heme trigger the conformational change of crystalline nitrite reductase?
  J Biol Chem, 274, 14997-15004.
PDB codes: 1n15 1n50 1n90
10360953 E.K.Wilson, A.Bellelli, S.Liberti, M.Arese, S.Grasso, F.Cutruzzolà, M.Brunori, and P.Brzezinski (1999).
Internal electron transfer and structural dynamics of cd1 nitrite reductase revealed by laser CO photodissociation.
  Biochemistry, 38, 7556-7564.  
10320660 F.Cutruzzolà (1999).
Bacterial nitric oxide synthesis.
  Biochim Biophys Acta, 1411, 231-249.  
9760233 D.Nurizzo, F.Cutruzzolà, M.Arese, D.Bourgeois, M.Brunori, C.Cambillau, and M.Tegoni (1998).
Conformational changes occurring upon reduction and NO binding in nitrite reductase from Pseudomonas aeruginosa.
  Biochemistry, 37, 13987-13996.
PDB codes: 1bl9 1nno
9667932 S.J.Ferguson (1998).
Nitrogen cycle enzymology.
  Curr Opin Chem Biol, 2, 182-193.  
9628486 S.Wang, W.R.Trumble, H.Liao, C.R.Wesson, A.K.Dunker, and C.H.Kang (1998).
Crystal structure of calsequestrin from rabbit skeletal muscle sarcoplasmic reticulum.
  Nat Struct Biol, 5, 476-483.
PDB code: 1a8y
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.