2JIQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes the Sixth Coordination of the Catalytic Molybdenum.

Najmudin, S.Gonzalez, P.J.Trincao, J.Coelho, C.Mukhopadhyay, A.Cerqueira, N.M.F.S.A.Romao, C.C.Moura, I.Moura, J.J.G.Brondino, C.D.Romao, M.J.

(2008) J.Biol.Inorg.Chem. 13: 737

  • DOI: 10.1007/s00775-008-0359-6
  • Primary Citation of Related Structures:  2JIM, 2JIO, 2JIP, 2JIR, 2V3V, 2V45

  • PubMed Abstract: 
  • 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 ...

    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.


    Related Citations: 
    • Epr and Redox Properties of Periplasmic Nitrate Reductase from Desulfovibrio Desulfuricans Atcc 27774
      Gonzalez, P.J.,Rivas, M.G.,Brondino, C.D.,Bursakov, S.A.,Moura, I.,Moura, J.J.G.
      (2006) J.Biol.Inorg.Chem. 11: 609


    Organizational Affiliation

    Departamento de QuĂ­mica, FCT-UNL, REQUIMTE/CQFB, Monte de Caparica, 2829-516, Almada, Portugal. shabir@dq.fct.unl.pt




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC NITRATE REDUCTASE
A
723Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)Gene Names: napA (nap)
EC: 1.7.99.4
Find proteins for P81186 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949))
Go to UniProtKB:  P81186
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MO
Query on MO

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A
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
NO2
Query on NO2

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A
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
NO3
Query on NO3

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A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
MGD
Query on MGD

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A
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.155 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.212α = 90.00
b = 105.212β = 90.00
c = 130.685γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance