5FC9

Novel Purple Cupredoxin from Nitrosopumilus maritimus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site.

Hosseinzadeh, P.Tian, S.Marshall, N.M.Hemp, J.Mullen, T.Nilges, M.J.Gao, Y.G.Robinson, H.Stahl, D.A.Gennis, R.B.Lu, Y.

(2016) J.Am.Chem.Soc. 138: 6324-6327

  • DOI: 10.1021/jacs.5b13128

  • PubMed Abstract: 
  • Mononuclear cupredoxin proteins usually contain a coordinately saturated type 1 copper (T1Cu) center and function exclusively as electron carriers. Here we report a cupredoxin isolated from the nitrifying archaeon Nitrosopumilus maritimus SCM1, calle ...

    Mononuclear cupredoxin proteins usually contain a coordinately saturated type 1 copper (T1Cu) center and function exclusively as electron carriers. Here we report a cupredoxin isolated from the nitrifying archaeon Nitrosopumilus maritimus SCM1, called Nmar1307, that contains a T1Cu center with an open binding site containing water. It displays a deep purple color due to strong absorptions around 413 nm (1880 M(-1) cm(-1)) and 558 nm (2290 M(-1) cm(-1)) in the UV-vis electronic spectrum. EPR studies suggest the protein contains two Cu(II) species of nearly equal population, one nearly axial, with hyperfine constant A∥ = 98 × 10(-4) cm(-1), and another more rhombic, with a smaller A∥ value of 69 × 10(-4) cm(-1). The X-ray crystal structure at 1.6 Å resolution confirms that it contains a Cu atom coordinated by two His and one Cys in a trigonal plane, with an axial H2O at 2.25 Å. Both UV-vis absorption and EPR spectroscopic studies suggest that the Nmar1307 can oxidize NO to nitrite, an activity that is attributable to the high reduction potential (354 mV vs SHE) of the copper site. These results suggest that mononuclear cupredoxins can have a wide range of structural features, including an open binding site containing water, making this class of proteins even more versatile.


    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory , Upton, New York 11973-5000, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Blue (Type 1) copper domain protein
A, B, C, D
95Nitrosopumilus maritimus (strain SCM1)Mutation(s): 0 
Find proteins for A9A2G4 (Nitrosopumilus maritimus (strain SCM1))
Go to UniProtKB:  A9A2G4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.887α = 90.00
b = 68.887β = 90.00
c = 184.450γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesCHE-1413328

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations