6UTQ

LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with cadmium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history. 


Literature

Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE.

Fellner, M., Huizenga, K.G., Hausinger, R.P., Hu, J.

(2020) Sci Rep 10: 5830-5830

  • DOI: https://doi.org/10.1038/s41598-020-62847-6
  • Primary Citation of Related Structures:  
    6UTP, 6UTQ, 6UTR, 6UTT

  • PubMed Abstract: 

    Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca 2+ , Mn 2+ , Fe 2+ /Fe 3+ , Co 2+ , Ni 2+ , Cu 2+ , Zn 2+ , and Cd 2+ , but not monovalent metal ions, Cr 3+ , Mg 2+ , Y 3+ , Sr 2+ or Ba 2+ . Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.

    • Organizational Affiliation: 

    Biochemistry, University of Otago, Dunedin, Otago, 9054, New Zealand.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent sacrificial sulfur transferase LarE
A, B, C, D, E
A, B, C, D, E, F
286Lactiplantibacillus plantarumMutation(s): 0 
Gene Names: 
UniProt
Find proteins for F9UST4 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Explore F9UST4 
Go to UniProtKB:  F9UST4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF9UST4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD (Subject of Investigation/LOI)
Query on CD
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
L [auth B]
M [auth B]
P [auth C]
G [auth A],
H [auth A],
L [auth B],
M [auth B],
P [auth C],
S [auth D],
T [auth D]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
O [auth B]
R [auth C]
V [auth D]
J [auth A],
K [auth A],
O [auth B],
R [auth C],
V [auth D],
X [auth E],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4
Download Ideal Coordinates CCD File 
I [auth A]
N [auth B]
Q [auth C]
U [auth D]
W [auth E]
I [auth A],
N [auth B],
Q [auth C],
U [auth D],
W [auth E],
Y [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.775α = 90
b = 107.775β = 90
c = 319.633γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1516126

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2020-04-15
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description