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 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1007/s00775-008-0359-6
  • Primary Citation of Related Structures:  
    2JIM, 2JIO, 2JIP, 2JIQ, 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PERIPLASMIC NITRATE REDUCTASE723Desulfovibrio desulfuricansMutation(s): 0 
EC: 1.7.99.4
UniProt
Find proteins for P81186 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore P81186 
Go to UniProtKB:  P81186
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81186
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download Ideal Coordinates CCD File 
D [auth A],
E [auth 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
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
SF4
Query on SF4

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B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MO
Query on MO

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C [auth A]MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
NO3
Query on NO3

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H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
NO2
Query on NO2

Download Ideal Coordinates CCD File 
G [auth A]NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
UNX
Query on UNX

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F [auth A]UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.212α = 90
b = 105.212β = 90
c = 130.685γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description