6X1O

WOR5 from Pyrococcus furiosus, as crystallized


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

An unprecedented function for a tungsten-containing oxidoreductase.

Mathew, L.G.Haja, D.K.Pritchett, C.McCormick, W.Zeineddine, R.Fontenot, L.S.Rivera, M.E.Glushka, J.Adams, M.W.W.Lanzilotta, W.N.

(2022) J Biol Inorg Chem 27: 747-758

  • DOI: https://doi.org/10.1007/s00775-022-01965-0
  • Primary Citation of Related Structures:  
    6X1O, 6X6U

  • PubMed Abstract: 

    Five tungstopterin-containing oxidoreductases were characterized from the hyperthermophile Pyrococcus furiosus. Each enzyme catalyzes the reversible conversion of one or more aldehydes to the corresponding carboxylic acid, but they have different specificities. The physiological functions of only two of these enzymes are known: one, termed GAPOR, is a glycolytic enzyme that oxidizes glyceraldehyde-3-phosphate, while the other, termed AOR, oxidizes multiple aldehydes generated during peptide fermentation. Two of the enzymes have known structures (AOR and FOR). Herein, we focus on WOR5, the fifth tungstopterin enzyme to be discovered in P. furiosus. Expression of WOR5 was previously shown to be increased during cold shock (growth at 72 ℃), although the physiological substrate is not known. To gain insight into WOR5 function, we sought to determine both its structure and identify its intracellular substrate. Crystallization experiments were performed with a concentrated cytoplasmic extract of P. furiosus grown at 72 ℃ and the structure of WOR5 was deduced from the crystals that were obtained. In contrast to a previous report, WOR5 is heterodimeric containing an additional polyferredoxin-like subunit with four [4Fe-4S] clusters. The active site structure of WOR5 is substantially different from that of AOR and FOR and the significant electron density observed adjacent to the tungsten cofactor of WOR5 was modeled as an aliphatic sulfonate. Biochemical assays and product analysis confirmed that WOR5 is an aliphatic sulfonate ferredoxin oxidoreductase (ASOR). A catalytic mechanism for ASOR is proposed based on the structural information and the potential role of ASOR in the cold-shock response is discussed.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formaldehyde:ferredoxin oxidoreductase wor5
A, C
624Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06635
UniProt
Find proteins for I6V2C3 (Pyrococcus furiosus COM1)
Explore I6V2C3 
Go to UniProtKB:  I6V2C3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6V2C3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidoreductase, Fe-S subunit
B, D
166Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_06630
UniProt
Find proteins for I6U881 (Pyrococcus furiosus COM1)
Explore I6U881 
Go to UniProtKB:  I6U881
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6U881
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTE
Query on PTE

Download Ideal Coordinates CCD File 
F [auth A],
Q [auth C]
TUNGSTOPTERIN COFACTOR
C20 H29 Mg N10 O14 P2 S4 W
PZGYSZZGRVZGLK-MAAILCHMSA-K
SF4
Query on SF4

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G [auth A]
L [auth B]
M [auth B]
N [auth B]
O [auth B]
G [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
R [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UKM
Query on UKM

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E [auth A],
P [auth C]
(1R)-1-hydroxybutane-1-sulfonic acid
C4 H10 O4 S
KMBRJVMBQNMRDM-SCSAIBSYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth A],
U [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

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K [auth B],
V [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
S [auth C],
T [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.092α = 90
b = 126.821β = 90
c = 141.289γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references