PDBsum entry 2jio

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Oxidoreductase PDB id
Protein chain
720 a.a. *
MGD ×2
Waters ×810
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: A new catalytic mechanism of periplasmic nitrate reductase from desulfovibrio desulfuricans atcc 27774 from crystallographic and epr data and based on detailed analysis of the sixth ligand
Structure: Periplasmic nitrate reductase. Chain: a. Ec:
Source: Desulfovibrio desulfuricans. Organism_taxid: 876. Atcc: 27774
2.20Å     R-factor:   0.153     R-free:   0.209
Authors: S.Najmudin,P.J.Gonzalez,J.Trincao,C.Coelho,A.Mukhopadhyay,C. I.Moura,J.J.G.Moura,C.D.Brondino,M.J.Romao
Key ref: S.Najmudin et al. (2008). Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum. J Biol Inorg Chem, 13, 737-753. PubMed id: 18327621
28-Jun-07     Release date:   18-Mar-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P81186  (NAPA_DESDA) -  Periplasmic nitrate reductase
755 a.a.
720 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Nitrate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nitrite + acceptor = nitrate + reduced acceptor
+ 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    
J Biol Inorg Chem 13:737-753 (2008)
PubMed id: 18327621  
Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum.
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, M.J.Romão.
Nitrate reductase from Desulfovibrio desulfuricans ATCC 27774 (DdNapA) is a monomeric protein of 80 kDa harboring a bis(molybdopterin guanine dinucleotide) active site and a [4Fe-4S] cluster. Previous electron paramagnetic resonance (EPR) studies in both catalytic and inhibiting conditions showed that the molybdenum center has high coordination flexibility when reacted with reducing agents, substrates or inhibitors. As-prepared DdNapA samples, as well as those reacted with substrates and inhibitors, were crystallized and the corresponding structures were solved at resolutions ranging from 1.99 to 2.45 A. The good quality of the diffraction data allowed us to perform a detailed structural study of the active site and, on that basis, the sixth molybdenum ligand, originally proposed to be an OH/OH(2) ligand, was assigned as a sulfur atom after refinement and analysis of the B factors of all the structures. This unexpected result was confirmed by a single-wavelength anomalous diffraction experiment below the iron edge (lambda = 1.77 A) of the as-purified enzyme. Furthermore, for six of the seven datasets, the S-S distance between the sulfur ligand and the Sgamma atom of the molybdenum ligand Cys(A140) was substantially shorter than the van der Waals contact distance and varies between 2.2 and 2.85 A, indicating a partial disulfide bond. Preliminary EPR studies under catalytic conditions showed an EPR signal designated as a turnover signal (g values 1.999, 1.990, 1.982) showing hyperfine structure originating from a nucleus of unknown nature. Spectropotentiometric studies show that reduced methyl viologen, the electron donor used in the catalytic reaction, does not interact directly with the redox cofactors. The turnover signal can be obtained only in the presence of the reaction substrates. With use of the optimized conditions determined by spectropotentiometric titration, the turnover signal was developed with (15)N-labeled nitrate and in D(2)O-exchanged DdNapA samples. These studies indicate that this signal is not associated with a Mo(V)-nitrate adduct and that the hyperfine structure originates from two equivalent solvent-exchangeable protons. The new coordination sphere of molybdenum proposed on the basis of our studies led us to revise the currently accepted reaction mechanism for periplasmic nitrate reductases. Proposals for a new mechanism are discussed taking into account a molybdenum and ligand-based redox chemistry, rather than the currently accepted redox chemistry based solely on the molybdenum atom.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.  
19259562 A.Majumdar, K.Pal, and S.Sarkar (2009).
Necessity of fine tuning in Mo(iv) bis(dithiolene) complexes to warrant nitrate reduction.
  Dalton Trans, (), 1927-1938.  
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.  
18704520 C.Correia, S.Besson, C.D.Brondino, P.J.González, G.Fauque, J.Lampreia, I.Moura, and J.J.Moura (2008).
Biochemical and spectroscopic characterization of the membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617.
  J Biol Inorg Chem, 13, 1321-1333.  
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.