6X6U | pdb_00006x6u

WOR5 from Pyrococcus furiosus, taurine-bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 184.24 kDa 
  • Atom Count: 13,467 
  • Modeled Residue Count: 1,580 
  • Deposited Residue Count: 1,592 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Formaldehyde:ferredoxin oxidoreductase wor5
A, C
623Pyrococcus 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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxidoreductase, Fe-S subunit
B, D
173Pyrococcus 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
E [auth A],
S [auth C]
TUNGSTOPTERIN COFACTOR
C20 H22 Mg N10 O14 P2 S4 W
DYJJSYQWWQOQKE-MAAILCHMSA-F
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
F [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
F [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
T [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
TAU

Query on TAU



Download:Ideal Coordinates CCD File
I [auth A],
X [auth C]
2-AMINOETHANESULFONIC ACID
C2 H7 N O3 S
XOAAWQZATWQOTB-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
FA [auth D]
J [auth A]
K [auth A]
L [auth A]
R [auth B]
FA [auth D],
J [auth A],
K [auth A],
L [auth A],
R [auth B],
Y [auth C],
Z [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL

Query on CL



Download:Ideal Coordinates CCD File
EA [auth D],
Q [auth B],
W [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
U [auth C],
V [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.148α = 90
b = 127.501β = 90
c = 140.712γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection