4YDD

Crystal structure of the perchlorate reductase PcrAB from Azospira suillum PS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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: https://doi.org/10.1074/jbc.M116.714618
  • Primary Citation of Related Structures:  
    4YDD, 5CH7, 5CHC, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DMSO reductase family type II enzyme, molybdopterin subunit
A, C, E
899Azospira oryzae PSMutation(s): 0 
UniProt
Find proteins for G8QM55 (Azospira oryzae (strain ATCC BAA-33 / DSM 13638 / PS))
Explore G8QM55 
Go to UniProtKB:  G8QM55
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8QM55
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DMSO reductase family type II enzyme, iron-sulfur subunit
B, D, F
333Azospira oryzae PSMutation(s): 0 
UniProt
Find proteins for G8QM54 (Azospira oryzae (strain ATCC BAA-33 / DSM 13638 / PS))
Explore G8QM54 
Go to UniProtKB:  G8QM54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8QM54
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MD1
Query on MD1

Download Ideal Coordinates CCD File 
AA [auth C],
J [auth A],
NA [auth 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
MGD
Query on MGD

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

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G [auth A]
GA [auth D]
HA [auth D]
IA [auth D]
KA [auth E]
G [auth A],
GA [auth D],
HA [auth D],
IA [auth D],
KA [auth E],
R [auth B],
S [auth B],
T [auth B],
VA [auth F],
WA [auth F],
X [auth C],
XA [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

Download Ideal Coordinates CCD File 
FA [auth D],
Q [auth B],
UA [auth F]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
PEG
Query on PEG

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EA [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MO
Query on MO

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H [auth A],
LA [auth E],
Y [auth C]
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
GOL
Query on GOL

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CA [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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BA [auth C]
DA [auth C]
JA [auth D]
K [auth A]
L [auth A]
BA [auth C],
DA [auth C],
JA [auth D],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
OA [auth E],
P [auth A],
PA [auth E],
QA [auth E],
RA [auth E],
SA [auth E],
TA [auth E],
U [auth B],
V [auth B],
YA [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

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W [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.827α = 90
b = 175.501β = 90
c = 193.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2016-05-11
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description