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PDBsum entry 1y5i

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1y5i
Jmol
Contents
Protein chains
1244 a.a. *
509 a.a. *
217 a.a. *
Ligands
MD1 ×2
SF4 ×4
F3S
3PH
HEM ×2
AGA
Metals
6MO
Waters ×1118
* Residue conservation analysis
PDB id:
1y5i
Name: Oxidoreductase
Title: The crystal structure of the narghi mutant nari-k86a
Structure: Respiratory nitrate reductase 1 alpha chain. Chain: a. Synonym: narg, nitrate reductase a alpha subunit, quinol- nitrate oxidoreductase alpha subunit. Engineered: yes. Respiratory nitrate reductase 1 beta chain. Chain: b. Synonym: narh, nitrate reductase a beta subunit, quinol- nitrate oxidoreductase beta subunit.
Source: Escherichia coli. Organism_taxid: 562. Gene: narg. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: narh. Gene: nari.
Biol. unit: Hexamer (from PQS)
Resolution:
1.90Å     R-factor:   0.176     R-free:   0.208
Authors: M.G.Bertero,R.A.Rothery,N.Boroumand,M.Palak,F.Blasco, N.Ginet,J.H.Weiner,N.C.J.Strynadka
Key ref:
M.G.Bertero et al. (2005). Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A. J Biol Chem, 280, 14836-14843. PubMed id: 15615728 DOI: 10.1074/jbc.M410457200
Date:
02-Dec-04     Release date:   08-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09152  (NARG_ECOLI) -  Respiratory nitrate reductase 1 alpha chain
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1247 a.a.
1244 a.a.
Protein chain
Pfam   ArchSchema ?
P11349  (NARH_ECOLI) -  Respiratory nitrate reductase 1 beta chain
Seq:
Struc:
512 a.a.
509 a.a.
Protein chain
Pfam   ArchSchema ?
P11350  (NARI_ECOLI) -  Respiratory nitrate reductase 1 gamma chain
Seq:
Struc:
225 a.a.
217 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: 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     membrane   5 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     electron carrier activity     10 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M410457200 J Biol Chem 280:14836-14843 (2005)
PubMed id: 15615728  
 
 
Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A.
M.G.Bertero, R.A.Rothery, N.Boroumand, M.Palak, F.Blasco, N.Ginet, J.H.Weiner, N.C.Strynadka.
 
  ABSTRACT  
 
The crystal structure of Escherichia coli nitrate reductase A (NarGHI) in complex with pentachlorophenol has been determined to 2.0 A of resolution. We have shown that pentachlorophenol is a potent inhibitor of quinol:nitrate oxidoreductase activity and that it also perturbs the EPR spectrum of one of the hemes located in the membrane anchoring subunit (NarI). This new structural information together with site-directed mutagenesis data, biochemical analyses, and molecular modeling provide the first molecular characterization of a quinol binding and oxidation site (Q-site) in NarGHI. A possible proton conduction pathway linked to electron transfer reactions has also been defined, providing fundamental atomic details of ubiquinol oxidation by NarGHI at the bacterial membrane.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Chemical structures for menaquinol (a), ubiquinol (b), pentachlorophenol (c), 2-n-heptyl-4-hydroxyquinoline-N-oxide (d), and plumbagin (e).
Figure 7.
FIG. 7. Structure of the mutant NarGHI-H66Y. Ribbon representation of NarI bearing the mutation His-66 to Tyr viewed parallel to the membrane.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 14836-14843) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21186382 P.V.Bernhardt (2011).
Exploiting the versatility and selectivity of Mo enzymes with electrochemistry.
  Chem Commun (Camb), 47, 1663-1673.  
21518899 R.Arias-Cartin, S.Grimaldi, J.Pommier, P.Lanciano, C.Schaefer, P.Arnoux, G.Giordano, B.Guigliarelli, and A.Magalon (2011).
Cardiolipin-based respiratory complex activation in bacteria.
  Proc Natl Acad Sci U S A, 108, 7781-7786.  
20484676 K.Möbius, R.Arias-Cartin, D.Breckau, A.L.Hännig, K.Riedmann, R.Biedendieck, S.Schröder, D.Becher, A.Magalon, J.Moser, M.Jahn, and D.Jahn (2010).
Heme biosynthesis is coupled to electron transport chains for energy generation.
  Proc Natl Acad Sci U S A, 107, 10436-10441.  
19892705 S.Grimaldi, R.Arias-Cartin, P.Lanciano, S.Lyubenova, B.Endeward, T.F.Prisner, A.Magalon, and B.Guigliarelli (2010).
Direct evidence for nitrogen ligation to the high stability semiquinone intermediate in Escherichia coli nitrate reductase A.
  J Biol Chem, 285, 179-187.  
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.  
18535145 G.J.Workun, K.Moquin, R.A.Rothery, and J.H.Weiner (2008).
Evolutionary persistence of the molybdopyranopterin-containing sulfite oxidase protein fold.
  Microbiol Mol Biol Rev, 72, 228.  
17139260 M.L.Rodrigues, T.F.Oliveira, I.A.Pereira, and M.Archer (2006).
X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination.
  EMBO J, 25, 5951-5960.
PDB code: 2j7a
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.