5CH7 | pdb_00005ch7

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

• PDB DOI: https://doi.org/10.2210/pdb5CH7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Azospira oryzae PS
• Mutation(s): No 


• Deposited: 2015-07-10 Released: 2016-03-09 
• Deposition Author(s): Tsai, C.-L., Tainer, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.233 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

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 Biological Chem 291: 9190-9202

• PubMed: 26940877 
• DOI: https://doi.org/10.1074/jbc.M116.714618
• Primary Citation 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.

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Organizational Affiliation: 
• From the Energy Biosciences Institute and.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030.
From the Energy Biosciences Institute and Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, SAXS

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, SAXS

Macromolecule Content 

• Total Structure Weight: 429.08 kDa 
• Atom Count: 31,660 
• Modeled Residue Count: 3,661 
• Deposited Residue Count: 3,696 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DMSO reductase family type II enzyme, molybdopterin subunit	A, C, E	899	Azospira oryzae PS	Mutation(s): 0
UniProt
Find proteins for G8QM55 (Azospira oryzae (strain ATCC BAA-33 / DSM 13638 / PS)) Explore G8QM55  Go to UniProtKB:  G8QM55

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DMSO reductase family type II enzyme, iron-sulfur subunit	B, D, F	333	Azospira oryzae PS	Mutation(s): 0
UniProt
Find proteins for G8QM54 (Azospira oryzae (strain ATCC BAA-33 / DSM 13638 / PS)) Explore G8QM54  Go to UniProtKB:  G8QM54

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MD1	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
MGD	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
SF4	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-UHFFFAOYSA-N
F3S	BB [auth F], MA [auth D], T [auth B]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
MO	BA [auth C], H [auth A], SA [auth E]	MOLYBDENUM ATOM Mo ZOKXTWBITQBERF-UHFFFAOYSA-N
GOL	P [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
SO3	IA [auth C], JA [auth C], Q [auth A], S [auth A], YA [auth E]	SULFITE ION O3 S LSNNMFCWUKXFEE-UHFFFAOYSA-L
ZN	AB [auth E], KA [auth C], O [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	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
ACT	HA [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	GA [auth C], HB [auth F], N [auth A], ZA [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.233 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.884	α = 90
b = 175.667	β = 90
c = 193.278	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Tsai, C.-L., Tainer, J.A.

Revision History  

• 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
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2026-03-04
  Changes: Refinement description, Structure summary