spacer
spacer

PDBsum entry 1fgj

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1fgj
Jmol
Contents
Protein chains
499 a.a. *
Ligands
HEM ×14
HEC ×2
* Residue conservation analysis
PDB id:
1fgj
Name: Oxidoreductase
Title: X-ray structure of hydroxylamine oxidoreductase
Structure: Hydroxylamine oxidoreductase. Chain: a, b. Ec: 1.7.3.4
Source: Nitrosomonas europaea. Organism_taxid: 915. Atcc: 19178
Biol. unit: Trimer (from PQS)
Resolution:
2.80Å     R-factor:   0.230     R-free:   0.309
Authors: N.Tanaka,N.Igarashi,H.Moriyama
Key ref: N.Igarashi et al. (1997). The 2.8 A structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea. Nat Struct Biol, 4, 276-284. PubMed id: 9095195
Date:
03-Mar-97     Release date:   04-Mar-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q50925  (HAO_NITEU) -  Hydroxylamine oxidoreductase
Seq:
Struc:
 
Seq:
Struc:
570 a.a.
499 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.7.2.6  - Hydroxylamine dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. Hydroxylamine + H2O + 2 ferricytochrome c = nitrite + 2 ferrocytochrome c + 5 H+
2. Hydroxylamine + ferricytochrome c = nitric oxide + ferrocytochrome c + 3 H+
Hydroxylamine
+ H(2)O
+ 2 × ferricytochrome c
= nitrite
+ 2 × ferrocytochrome c
+ 5 × H(+)
Hydroxylamine
+ ferricytochrome c
= nitric oxide
+ ferrocytochrome c
+ 3 × H(+)
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
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   2 terms 
  Biochemical function     oxidoreductase activity     2 terms  

 

 
    reference    
 
 
Nat Struct Biol 4:276-284 (1997)
PubMed id: 9095195  
 
 
The 2.8 A structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea.
N.Igarashi, H.Moriyama, T.Fujiwara, Y.Fukumori, N.Tanaka.
 
  ABSTRACT  
 
The 2.8 A crystal structure of hydroxylamine oxidoreductase of a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea, is described. Twenty-four haems lie in the centre bottom of the trimeric molecule, localized in four clusters within each monomer. The haem clusters within the trimer are aligned to form a ring that has inlet and outlet sites. The inlet is occupied by a novel haem, P460, and there are two possible outlet sites per monomer formed by paired haems lying within a cavity or cleft on the protein surface. The structure suggests pathways by which electron transfer may occur through the precisely arranged haems and provides a framework for the interpretation of previous and future biochemical and genetic observations.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265785 C.Lockwood, J.N.Butt, T.A.Clarke, and D.J.Richardson (2011).
Molecular interactions between multihaem cytochromes: probing the protein-protein interactions between pentahaem cytochromes of a nitrite reductase complex.
  Biochem Soc Trans, 39, 263-268.  
20544970 L.J.Smith, A.Kahraman, and J.M.Thornton (2010).
Heme proteins--diversity in structural characteristics, function, and folding.
  Proteins, 78, 2349-2368.  
19830422 P.Junier, V.Molina, C.Dorador, O.Hadas, O.S.Kim, T.Junier, J.P.Witzel, and J.F.Imhoff (2010).
Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment.
  Appl Microbiol Biotechnol, 85, 425-440.  
20084531 S.Sharma, G.Cavallaro, and A.Rosato (2010).
A systematic investigation of multiheme c-type cytochromes in prokaryotes.
  J Biol Inorg Chem, 15, 559-571.  
19197347 B.J.Campbell, J.L.Smith, T.E.Hanson, M.G.Klotz, L.Y.Stein, C.K.Lee, D.Wu, J.M.Robinson, H.M.Khouri, J.A.Eisen, and S.C.Cary (2009).
Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola.
  PLoS Genet, 5, e1000362.  
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.
  Biopolymers, 91, 1064-1082.  
18703849 D.Heitmann, and O.Einsle (2008).
Pseudo-merohedral twinning in crystals of the dihaem c-type cytochrome DHC2 from Geobacter sulfurreducens.
  Acta Crystallogr D Biol Crystallogr, 64, 993-999.  
18505274 H.J.Kim, A.Zatsman, A.K.Upadhyay, M.Whittaker, D.Bergmann, M.P.Hendrich, and A.B.Hooper (2008).
Membrane tetraheme cytochrome c(m552) of the ammonia-oxidizing nitrosomonas europaea: a ubiquinone reductase.
  Biochemistry, 47, 6539-6551.  
18553112 J.Kostera, M.D.Youngblut, J.M.Slosarczyk, and A.A.Pacheco (2008).
Kinetic and product distribution analysis of NO* reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase.
  J Biol Inorg Chem, 13, 1073-1083.  
18031536 M.G.Klotz, and L.Y.Stein (2008).
Nitrifier genomics and evolution of the nitrogen cycle.
  FEMS Microbiol Lett, 278, 146-156.  
19030605 S.E.Bowman, and K.L.Bren (2008).
The chemistry and biochemistry of heme c: functional bases for covalent attachment.
  Nat Prod Rep, 25, 1118-1130.  
17583915 A.R.Pearson, B.O.Elmore, C.Yang, J.D.Ferrara, A.B.Hooper, and C.M.Wilmot (2007).
The crystal structure of cytochrome P460 of Nitrosomonas europaea reveals a novel cytochrome fold and heme-protein cross-link.
  Biochemistry, 46, 8340-8349.
PDB codes: 2je2 2je3
17506671 D.J.Arp, P.S.Chain, and M.G.Klotz (2007).
The impact of genome analyses on our understanding of ammonia-oxidizing bacteria.
  Annu Rev Microbiol, 61, 503-528.  
17372351 K.Fukuyama, and T.Okada (2007).
Structures of cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosusperoxidase at 100 K refined to 1.3 A resolution: coordination geometries of the ligands to the haem iron.
  Acta Crystallogr D Biol Crystallogr, 63, 472-477.
PDB codes: 2e39 2e3a 2e3b
17172456 M.Shimamura, T.Nishiyama, H.Shigetomo, T.Toyomoto, Y.Kawahara, K.Furukawa, and T.Fujii (2007).
Isolation of a multiheme protein with features of a hydrazine-oxidizing enzyme from an anaerobic ammonium-oxidizing enrichment culture.
  Appl Environ Microbiol, 73, 1065-1072.  
16569009 A.K.Upadhyay, A.B.Hooper, and M.P.Hendrich (2006).
NO reductase activity of the tetraheme cytochrome C554 of Nitrosomonas europaea.
  J Am Chem Soc, 128, 4330-4337.  
  16582494 B.O.Elmore, A.R.Pearson, C.M.Wilmot, and A.B.Hooper (2006).
Expression, purification, crystallization and preliminary X-ray diffraction of a novel Nitrosomonas europaea cytochrome, cytochrome P460.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 395-398.  
16790931 R.C.Hillig, and L.Renault (2006).
Detecting and overcoming hemihedral twinning during the MIR structure determination of Rna1p.
  Acta Crystallogr D Biol Crystallogr, 62, 750-765.
PDB code: 2ca6
16234915 C.G.Mowat, and S.K.Chapman (2005).
Multi-heme cytochromes--new structures, new chemistry.
  Dalton Trans, (), 3381-3389.  
16151127 D.J.Bergmann, A.B.Hooper, and M.G.Klotz (2005).
Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history.
  Appl Environ Microbiol, 71, 5371-5382.  
15361860 C.G.Mowat, E.Rothery, C.S.Miles, L.McIver, M.K.Doherty, K.Drewette, P.Taylor, M.D.Walkinshaw, S.K.Chapman, and G.A.Reid (2004).
Octaheme tetrathionate reductase is a respiratory enzyme with novel heme ligation.
  Nat Struct Mol Biol, 11, 1023-1024.
PDB code: 1sp3
12709052 D.J.Bergmann, and A.B.Hooper (2003).
Cytochrome P460 of Nitrosomonas europaea. Formation of the heme-lysine cross-link in a heterologous host and mutagenic conversion to a non-cross-linked cytochrome c'.
  Eur J Biochem, 270, 1935-1941.  
12594933 J.W.Allen, O.Daltrop, J.M.Stevens, and S.J.Ferguson (2003).
C-type cytochromes: diverse structures and biogenesis systems pose evolutionary problems.
  Philos Trans R Soc Lond B Biol Sci, 358, 255-266.  
11939777 A.Brigé, D.Leys, T.E.Meyer, M.A.Cusanovich, and J.J.Van Beeumen (2002).
The 1.25 A resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.
  Biochemistry, 41, 4827-4836.
PDB code: 1jni
12080059 D.Leys, T.E.Meyer, A.S.Tsapin, K.H.Nealson, M.A.Cusanovich, and J.J.Van Beeumen (2002).
Crystal structures at atomic resolution reveal the novel concept of "electron-harvesting" as a role for the small tetraheme cytochrome c.
  J Biol Chem, 277, 35703-35711.
PDB codes: 1m1p 1m1q 1m1r
12165429 J.Simon (2002).
Enzymology and bioenergetics of respiratory nitrite ammonification.
  FEMS Microbiol Rev, 26, 285-309.  
12048216 J.W.Allen, E.J.Tomlinson, L.Hong, and S.J.Ferguson (2002).
The Escherichia coli cytochrome c maturation (Ccm) system does not detectably attach heme to single cysteine variants of an apocytochrome c.
  J Biol Chem, 277, 33559-33563.  
12042067 M.Paoli, J.Marles-Wright, and A.Smith (2002).
Structure-function relationships in heme-proteins.
  DNA Cell Biol, 21, 271-280.  
12060734 O.Daltrop, J.W.Allen, A.C.Willis, and S.J.Ferguson (2002).
In vitro formation of a c-type cytochrome.
  Proc Natl Acad Sci U S A, 99, 7872-7876.  
11863430 V.A.Bamford, H.C.Angove, H.E.Seward, A.J.Thomson, J.A.Cole, J.N.Butt, A.M.Hemmings, and D.J.Richardson (2002).
Structure and spectroscopy of the periplasmic cytochrome c nitrite reductase from Escherichia coli.
  Biochemistry, 41, 2921-2931.
PDB code: 1gu6
11180062 L.Poughon, C.G.Dussap, and J.B.Gros (2001).
Energy model and metabolic flux analysis for autotrophic nitrifiers.
  Biotechnol Bioeng, 72, 416-433.  
11358521 O.Einsle, S.Foerster, K.Mann, G.Fritz, A.Messerschmidt, and P.M.Kroneck (2001).
Spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochrome c3 from Desulfovibrio desulfuricans Essex 6.
  Eur J Biochem, 268, 3028-3035.
PDB code: 1i77
11077158 H.Bothe, G.Jost, M.Schloter, B.B.Ward, and K.Witzel (2000).
Molecular analysis of ammonia oxidation and denitrification in natural environments.
  FEMS Microbiol Rev, 24, 673-690.  
10653813 J.N.Butt, J.Thornton, D.J.Richardson, and P.S.Dobbin (2000).
Voltammetry of a flavocytochrome c(3): the lowest potential heme modulates fumarate reduction rates.
  Biophys J, 78, 1001-1009.  
10820012 J.Schalk, S.de Vries, J.G.Kuenen, and M.S.Jetten (2000).
Involvement of a novel hydroxylamine oxidoreductase in anaerobic ammonium oxidation.
  Biochemistry, 39, 5405-5412.  
10722689 S.J.Field, P.S.Dobbin, M.R.Cheesman, N.J.Watmough, A.J.Thomson, and D.J.Richardson (2000).
Purification and magneto-optical spectroscopic characterization of cytoplasmic membrane and outer membrane multiheme c-type cytochromes from Shewanella frigidimarina NCIMB400.
  J Biol Chem, 275, 8515-8522.  
10348621 D.J.Richardson, and N.J.Watmough (1999).
Inorganic nitrogen metabolism in bacteria.
  Curr Opin Chem Biol, 3, 207-219.  
10647174 P.D.Barker, and S.J.Ferguson (1999).
Still a puzzle: why is haem covalently attached in c-type cytochromes?
  Structure, 7, R281-R290.  
10368280 P.M.Matias, R.Coelho, I.A.Pereira, A.V.Coelho, A.W.Thompson, L.C.Sieker, J.L.Gall, and M.A.Carrondo (1999).
The primary and three-dimensional structures of a nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774 reveal a new member of the Hmc family.
  Structure, 7, 119-130.
PDB code: 19hc
  9851984 D.J.Bergmann, J.A.Zahn, A.B.Hooper, and A.A.DiSpirito (1998).
Cytochrome P460 genes from the methanotroph Methylococcus capsulatus bath.
  J Bacteriol, 180, 6440-6445.  
9535866 J.Yu, and N.E.Le Brun (1998).
Studies of the cytochrome subunits of menaquinone:cytochrome c reductase (bc complex) of Bacillus subtilis. Evidence for the covalent attachment of heme to the cytochrome b subunit.
  J Biol Chem, 273, 8860-8866.  
9667932 S.J.Ferguson (1998).
Nitrogen cycle enzymology.
  Curr Opin Chem Biol, 2, 182-193.  
  9409151 W.G.Zumft (1997).
Cell biology and molecular basis of denitrification.
  Microbiol Mol Biol Rev, 61, 533-616.  
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.