6CZ9

The arsenate respiratory reductase (Arr) complex from Shewanella sp. ANA-3 bound to arsenite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations.

Glasser, N.R.Oyala, P.H.Osborne, T.H.Santini, J.M.Newman, D.K.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E8614-E8623

  • DOI: 10.1073/pnas.1807984115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we repor ...

    Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-Å resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 Å), the product arsenite (1.8 Å), and the natural inhibitor phosphate (1.7 Å). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit ( K m = 44.6 ± 1.6 μM, k cat = 9,810 ± 220 seconds -1 ), and phosphate is a competitive inhibitor of arsenate reduction ( K i = 325 ± 12 μM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that ( i ) arsenate desorption limits microbiologically induced arsenate reductive mobilization and ( ii ) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.


    Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125; dkn@caltech.edu.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125.,Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ArrA
A, C
814Shewanella sp. (strain ANA-3)Mutation(s): 0 
Gene Names: arrA
Find proteins for Q7WTU0 (Shewanella sp. (strain ANA-3))
Go to UniProtKB:  Q7WTU0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
4Fe-4S ferredoxin, iron-sulfur binding domain protein
B, D
234Shewanella sp. (strain ANA-3)Mutation(s): 0 
Gene Names: arrB
Find proteins for Q7WTT9 (Shewanella sp. (strain ANA-3))
Go to UniProtKB:  Q7WTT9
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, C, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PG5
Query on PG5

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Download CCD File 
A, C
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
C8 H18 O4
YFNKIDBQEZZDLK-UHFFFAOYSA-N
 Ligand Interaction
AST
Query on AST

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Download CCD File 
A, C
ARSENITE
As O3
OWTFKEBRIAXSMO-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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Download CCD File 
A, B, C
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MO
Query on MO

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A, C
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MGD
Query on MGD

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Download CCD File 
A, C
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: 1.8 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.142 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 232.512α = 90.00
b = 86.306β = 127.72
c = 147.367γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States5R01HL117328-03

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references
  • Version 1.2: 2018-09-19
    Type: Data collection, Database references
  • Version 1.3: 2018-10-03
    Type: Data collection, Database references
  • Version 1.4: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.5: 2019-12-04
    Type: Author supporting evidence