PDBsum entry 2nya

Oxidoreductase

PDB id: 2nya

Contents

Protein chains

791 a.a. *

Ligands

SF4 ×2

MGD ×4

Metals

6MO ×2

Waters ×925

* Residue conservation analysis

PDB id:

2nya

Name:

Oxidoreductase

Title:

Crystal structure of the periplasmic nitrate reductase (nap) from escherichia coli

Structure:

Periplasmic nitrate reductase. Chain: a, f. Engineered: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: napa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.184 R-free: 0.243

Authors:

B.J.N.Jepson,D.J.Richardson,A.M.Hemmings

Key ref:

B.J.Jepson et al. (2007). Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli. J Biol Chem, 282, 6425-6437. PubMed id: 17130127 DOI: 10.1074/jbc.M607353200

Date:

20-Nov-06 Release date: 05-Dec-06

Protein chains

P33937  (NAPA_ECOLI) -  Periplasmic nitrate reductase from Escherichia coli (strain K12)

Seq: 828 a.a.

Struc: 791 a.a.

Enzyme reactions

• Enzyme class: E.C.1.9.6.1 - nitrate reductase (cytochrome).
• Reaction: 2 Fe(II)-[cytochrome] + nitrate + 2 H⁺ = 2 Fe(III)-[cytochrome] + nitrite + H2O

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M607353200

J Biol Chem 282:6425-6437 (2007)

PubMed id: 17130127

Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli.

B.J.Jepson, S.Mohan, T.A.Clarke, A.J.Gates, J.A.Cole, C.S.Butler, J.N.Butt, A.M.Hemmings, D.J.Richardson.

ABSTRACT

The Escherichia coli NapA (periplasmic nitrate reductase) contains a [4Fe-4S] cluster and a Mo-bis-molybdopterin guanine dinucleotide cofactor. The NapA holoenzyme associates with a di-heme c-type cytochrome redox partner (NapB). These proteins have been purified and studied by spectropotentiometry, and the structure of NapA has been determined. In contrast to the well characterized heterodimeric NapAB systems ofalpha-proteobacteria, such as Rhodobacter sphaeroides and Paracoccus pantotrophus, the gamma-proteobacterial E. coli NapA and NapB proteins purify independently and not as a tight heterodimeric complex. This relatively weak interaction is reflected in dissociation constants of 15 and 32 mum determined for oxidized and reduced NapAB complexes, respectively. The surface electrostatic potential of E. coli NapA in the apparent NapB binding region is markedly less polar and anionic than that of the alpha-proteobacterial NapA, which may underlie the weaker binding of NapB. The molybdenum ion coordination sphere of E. coli NapA includes two molybdopterin guanine dinucleotide dithiolenes, a protein-derived cysteinyl ligand and an oxygen atom. The Mo-O bond length is 2.6 A, which is indicative of a water ligand. The potential range over which the Mo(6+) state is reduced to the Mo(5+) state in either NapA (between +100 and -100 mV) or the NapAB complex (-150 to -350 mV) is much lower than that reported for R. sphaeroides NapA (midpoint potential Mo(6+/5+) > +350 mV), and the form of the Mo(5+) EPR signal is quite distinct. In E. coli NapA or NapAB, the Mo(5+) state could not be further reduced to Mo(4+). We then propose a catalytic cycle for E. coli NapA in which nitrate binds to the Mo(5+) ion and where a stable des-oxo Mo(6+) species may participate.

Selected figure(s)

Figure 5.
FIGURE 5. Crystal structure of E. coli NapA. A, view of NapA from E. coli with the different domains colored as follows: domain I (residues 1–59, 492–520, and 590–630) in red; domain II (residues 60–138, 375–491, and 521–589) in green; domain III (residues 139–374) in yellow; and domain IV (residues 631–791) in blue. The regions colored gray are the extra loop regions not present in the D. desulfuricans NAP (9). The [4Fe-4S] cluster and the Mo-bis-MGD cofactors are shown in ball and stick format and are colored black. B, view of the 4Fe4S cluster and Mo-bis-MGD cofactor showing the conserved water molecule that is coordinated by Lys-47 and one of the MGD moieties.

Figure 6.
FIGURE 6. Electrostatic surface representations of the NAP structures. A, electrostatic surface of the molybdenum funnel face of the various NAP structures. B, electrostatic surface of the presumed NapB interaction face of the various NAP structures. Electrostatic surfaces were calculated in the program GRASP (28) and displayed in PYMOL (Delano Scientific). The "surface potentials" of color property scale -10 (red, negatively charged) to +10 (blue, positively charged). Coordinates for D. desulfuricans NAP, PDB file 2NAP. Coordinates for R. sphaeroides NapA, Protein Data Bank (PDB) file 1OGY. The structures of E. coli, D. desulfuricans, and R. sphaeroides were aligned using Swisspdbviewer 3.0 ("Magic Fit"). D.d, D. desulfuricans; E.c, E. coli, R.s, R. sphaeroides.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 6425-6437) copyright 2007.

Figures were selected by the author.