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PDBsum entry 1ogy

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1ogy
Jmol
Contents
Protein chains
(+ 2 more) 790 a.a. *
(+ 2 more) 127 a.a. *
Ligands
SF4 ×8
MGD ×16
HEC ×16
Metals
_MO ×8
* Residue conservation analysis
PDB id:
1ogy
Name: Oxidoreductase
Title: Crystal structure of the heterodimeric nitrate reductase from rhodobacter sphaeroides
Structure: Periplasmic nitrate reductase. Chain: a, c, e, g, i, k, m, o. Fragment: catalytic subunit, residues 30-831. Synonym: nitrate reductase. Engineered: yes. Diheme cytochromE C napb molecule: nitrate reductase. Chain: b, d, f, h, j, l, n, p. Fragment: cytochrome subunit, residues 25-154.
Source: Rhodobacter sphaeroides. Organism_taxid: 1063. Expressed in: rhodobacter sphaeroides. Expression_system_taxid: 1063. Expression_system_taxid: 1063
Biol. unit: Dimer (from PDB file)
Resolution:
3.20Å     R-factor:   0.250     R-free:   0.268
Authors: P.Arnoux,M.Sabaty,J.Alric,B.Frangioni,B.Guigliarelli, J.-M.Adriano,D.Pignol
Key ref:
P.Arnoux et al. (2003). Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase. Nat Struct Biol, 10, 928-934. PubMed id: 14528294 DOI: 10.1038/nsb994
Date:
19-May-03     Release date:   09-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q53176  (NAPA_RHOS4) -  Periplasmic nitrate reductase
Seq:
Struc:
 
Seq:
Struc:
831 a.a.
790 a.a.*
Protein chains
Pfam   ArchSchema ?
Q53177  (NAPB_RHOS4) -  Periplasmic nitrate reductase, electron transfer subunit
Seq:
Struc:
154 a.a.
127 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, C, E, G, I, K, N, O: E.C.1.7.99.4  - Nitrate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nitrite + acceptor = nitrate + reduced acceptor
Nitrite
+ 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     periplasmic space   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     electron carrier activity     8 terms  

 

 
    Added reference    
 
 
DOI no: 10.1038/nsb994 Nat Struct Biol 10:928-934 (2003)
PubMed id: 14528294  
 
 
Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase.
P.Arnoux, M.Sabaty, J.Alric, B.Frangioni, B.Guigliarelli, J.M.Adriano, D.Pignol.
 
  ABSTRACT  
 
The structure of the respiratory nitrate reductase (NapAB) from Rhodobacter sphaeroides, the periplasmic heterodimeric enzyme responsible for the first step in the denitrification process, has been determined at a resolution of 3.2 A. The di-heme electron transfer small subunit NapB binds to the large subunit with cluster of NapA. A total of 57 residues at the N- and C-terminal extremities of NapB adopt an extended conformation, embracing the NapA subunit and largely contributing to the total area of 5,900 A(2) buried in the complex. Complex formation was studied further by measuring the variation of the redox potentials of all the cofactors upon binding. The marked effects observed are interpreted in light of the three-dimensional structure and depict a plasticity that contributes to an efficient electron transfer in the complex from the heme I of NapB to the molybdenum catalytic site of NapA.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereo views of the overall fold of the NapAB complex. (a) NapA is represented as a white ribbon, and NapB is colored from blue to red from the N to the C terminus, respectively. Molybdenum and iron atoms are represented as CPK models. (b) The same view as in a, rotated by 90. NapB is white. The four structural domains of NapA are colored as follows: domain I, red; domain II, green; domain III, yellow; domain IV, blue. Domain definitions were taken from Dias et al9.
Figure 2.
Figure 2. Comparisons of NapAB complex with the structures of the uncomplexed subunits. (a) Ribbon diagram of the NapAB complex. NapA is colored according to the r.m.s. deviations obtained by a superposition with the structure of the monomeric NapA from D. desulfuricans: residues with r.m.s. deviation <1.5 are in gold, between 1.5 and 2 in orange and >2.0 in red. Sequence insertions are green. The NapB subunit is blue. (b) Superimposition of the NapAB structure (NapB is colored in red with the hemes in light colors, and the NapA subunit is represented according to its surface) with the structure of the proteolytic fragment of NapB from H. influenzae (in green with the hemes in dark colors).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 928-934) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265780 A.J.Gates, C.S.Butler, D.J.Richardson, and J.N.Butt (2011).
Electrocatalytic reduction of nitrate and selenate by NapAB.
  Biochem Soc Trans, 39, 236-242.  
21423952 A.J.Gates, G.L.Kemp, C.Y.To, J.Mann, S.J.Marritt, A.G.Mayes, D.J.Richardson, and J.N.Butt (2011).
The relationship between redox enzyme activity and electrochemical potential-cellular and mechanistic implications from protein film electrochemistry.
  Phys Chem Chem Phys, 13, 7720-7731.  
21419779 C.Coelho, P.J.González, J.G.Moura, I.Moura, J.Trincão, and M.João Romão (2011).
The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states.
  J Mol Biol, 408, 932-948.
PDB codes: 3ml1 3o5a
20038586 M.Sabaty, G.Adryanczyk, C.Roustan, S.Cuiné, C.Lamouroux, and D.Pignol (2010).
Coproporphyrin excretion and low thiol levels caused by point mutation in the Rhodobacter sphaeroides S-adenosylmethionine synthetase gene.
  J Bacteriol, 192, 1238-1248.  
19959582 P.J.Simpson, D.J.Richardson, and R.Codd (2010).
The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB.
  Microbiology, 156, 302-312.  
19387485 H.Gao, Z.K.Yang, S.Barua, S.B.Reed, M.F.Romine, K.H.Nealson, J.K.Fredrickson, J.M.Tiedje, and J.Zhou (2009).
Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA.
  ISME J, 3, 966-976.  
19484273 M.Hofmann (2009).
Density functional theory study of model complexes for the revised nitrate reductase active site in Desulfovibrio desulfuricans NapA.
  J Biol Inorg Chem, 14, 1023-1035.  
19452052 M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
  Dalton Trans, (), 4053-4068.  
19360810 N.M.Cerqueira, P.J.Gonzalez, C.D.Brondino, M.J.Romão, C.C.Romão, I.Moura, and J.J.Moura (2009).
The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase.
  J Comput Chem, 30, 2466-2484.  
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
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
  17554176 C.Coelho, P.J.González, J.Trincão, A.L.Carvalho, S.Najmudin, T.Hettman, S.Dieckman, J.J.Moura, I.Moura, and M.J.Romão (2007).
Heterodimeric nitrate reductase (NapAB) from Cupriavidus necator H16: purification, crystallization and preliminary X-ray analysis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 516-519.  
17636351 M.Hofmann (2007).
Density functional theory studies of model complexes for molybdenum-dependent nitrate reductase active sites.
  J Biol Inorg Chem, 12, 989.  
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
17050691 J.Zhang, F.E.Frerman, and J.J.Kim (2006).
Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
  Proc Natl Acad Sci U S A, 103, 16212-16217.
PDB codes: 2gmh 2gmj
16791644 P.J.González, M.G.Rivas, C.D.Brondino, S.A.Bursakov, I.Moura, and J.J.Moura (2006).
EPR and redox properties of periplasmic nitrate reductase from Desulfovibrio desulfuricans ATCC 27774.
  J Biol Inorg Chem, 11, 609-616.  
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.
  Dalton Trans, (), 3580-3586.  
15863498 U.Kappler, and S.Bailey (2005).
Molecular basis of intramolecular electron transfer in sulfite-oxidizing enzymes is revealed by high resolution structure of a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit.
  J Biol Chem, 280, 24999-25007.
PDB codes: 2blf 2bpb
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.
  J Biol Chem, 279, 32212-32218.  
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.
  J Biol Inorg Chem, 9, 791-799.  
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.