5CH7

Crystal structure of the perchlorate reductase PcrAB - Phe164 gate switch intermediate - from Azospira suillum PS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

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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 ...

    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 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, jdcoates@berkeley.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DMSO reductase family type II enzyme, molybdopterin subunitA, C, E899Azospira oryzae PSMutation(s): 0 
Gene Names: Dsui_0149
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DMSO reductase family type II enzyme, iron-sulfur subunitB, D, F333Azospira oryzae PSMutation(s): 0 
Gene Names: Dsui_0148
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MD1
Query on MD1

Download Ideal Coordinates CCD File 
DA [auth C],
J [auth A],
UA [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
 Ligand Interaction
MGD
Query on MGD

Download Ideal Coordinates CCD File 
CA [auth C],
I [auth A],
TA [auth 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
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
SF4
Query on SF4

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AA [auth C],
CB [auth F],
DB [auth F],
EB [auth F],
G [auth A],
AA [auth C],
CB [auth F],
DB [auth F],
EB [auth F],
G [auth A],
NA [auth D],
OA [auth D],
PA [auth D],
RA [auth E],
U [auth B],
V [auth B],
W [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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BB [auth F],
MA [auth D],
T [auth B]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
MO
Query on MO

Download Ideal Coordinates CCD File 
BA [auth C],
H [auth A],
SA [auth E]
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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P [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SO3
Query on SO3

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IA [auth C],
JA [auth C],
Q [auth A],
S [auth A],
YA [auth E]
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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AB [auth E],
KA [auth C],
O [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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EA [auth C],
FA [auth C],
FB [auth F],
GB [auth F],
K [auth A],
EA [auth C],
FA [auth C],
FB [auth F],
GB [auth F],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
QA [auth D],
R [auth A],
VA [auth E],
WA [auth E],
X [auth B],
XA [auth E],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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HA [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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GA [auth C],
HB [auth F],
N [auth A],
ZA [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.884α = 90
b = 175.667β = 90
c = 193.278γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

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: 2017-11-01
    Changes: Author supporting evidence, Database references, Derived calculations