5CHC

Crystal structure of the perchlorate reductase PcrAB - substrate analog SeO3 bound - from Azospira suillum PS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

Youngblut, M.D.Tsai, C.L.Clark, I.C.Carlson, H.K.Maglaqui, A.P.Gau-Pan, P.S.Redford, S.A.Wong, A.Tainer, J.A.Coates, J.D.

(2016) J.Biol.Chem. 291: 9190-9202

  • DOI: 10.1074/jbc.M116.714618
  • Primary Citation of Related Structures:  4YDD, 5CH7, 5E7O

  • PubMed Abstract: 
  • Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the b ...

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth.


    Organizational Affiliation

    From the Energy Biosciences Institute and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DMSO reductase family type II enzyme, molybdopterin subunit
A, C, E
899Dechlorosoma suillum (strain ATCC BAA-33 / DSM 13638 / PS)N/A
Find proteins for G8QM55 (Dechlorosoma suillum (strain ATCC BAA-33 / DSM 13638 / PS))
Go to UniProtKB:  G8QM55
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DMSO reductase family type II enzyme, iron-sulfur subunit
B, D, F
333Dechlorosoma suillum (strain ATCC BAA-33 / DSM 13638 / PS)N/A
Find proteins for G8QM54 (Dechlorosoma suillum (strain ATCC BAA-33 / DSM 13638 / PS))
Go to UniProtKB:  G8QM54
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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A, B, C, D, E, F
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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B, D, F
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
ZN
Query on ZN

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A, C, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BSY
Query on BSY

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A, C, E
BISELENITE ION
H O3 Se
MCAHWIHFGHIESP-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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A, B, C, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO3
Query on SO3

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A, C, E
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MD1
Query on MD1

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A, C, E
PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
C20 H26 N10 O13 P2 S2
IRGDLSAXQOKWLX-XHEYTWMPSA-N
 Ligand Interaction
MO
Query on MO

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

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A, B, C, D, E, F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MGD
Query on MGD

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A, C, E
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: 2.38 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 133.926α = 90.00
b = 176.022β = 90.00
c = 193.691γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references, Other
  • Version 1.2: 2016-05-11
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Author supporting evidence, Database references, Derived calculations