6UTP

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

• PDB DOI: https://doi.org/10.2210/pdb6UTP/pdb

• Classification: TRANSFERASE
• Organism(s): Lactiplantibacillus plantarum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-29 Released: 2019-11-06 
• Deposition Author(s): Fellner, M., Huizenga, K., Hausinger, R.P., Hu, J.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 0.298 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 

Starting Model: experimental

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

• PubMed: 32242052 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 192.2 kDa 
• Atom Count: 10,890 
• Modelled Residue Count: 1,451 
• Deposited Residue Count: 1,716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent sacrificial sulfur transferase LarE	A, B, C, D, E, F	286	Lactiplantibacillus plantarum	Mutation(s): 0  Gene Names:  larE, AVR82_02840, BIZ32_00440, CFM86_00460, CUR48_11145, E3O64_03880, IV39_GL000116, LPJSA22_00116, LpLQ80_00490, Nizo1839_0768, Nizo2891_3302 EC: 4.4.1.37
UniProt
Find proteins for F9UST4 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UST4  Go to UniProtKB:  F9UST4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth F], BA [auth F], J [auth A], K [auth A], L [auth A], N [auth B], Q [auth C], R [auth C], V [auth D], W [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	G [auth A], M [auth B], O [auth C], S [auth D], X [auth E], Y [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CO (Subject of Investigation/LOI)	H [auth A], I [auth A], P [auth C], T [auth D], U [auth D], Z [auth F]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 0.298 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.21	α = 90
b = 106.21	β = 90
c = 313.55	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Currently 6UTP does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Fellner, M., Huizenga, K., Hausinger, R.P., Hu, J.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1516126

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Derived calculations
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2020-04-15
  Changes: Database references
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description