6R1L | pdb_00006r1l

Crystal structure of LmrR with bound copper phenanthroline

• PDB DOI: https://doi.org/10.2210/pdb6R1L/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Lactococcus cremoris subsp. cremoris MG1363
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-14 Released: 2020-04-01 
• Deposition Author(s): Reddem, R., Thunnissen, A.M.W.H.
• Funding Organization(s): Netherlands Organisation for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.248 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Cofactor Binding Dynamics Influence the Catalytic Activity and Selectivity of an Artificial Metalloenzyme.

Villarino, L., Chordia, S., Alonso-Cotchico, L., Reddem, E., Zhou, Z., Thunnissen, A.M.W.H., Marechal, J.D., Roelfes, G.

(2020) ACS Catal 10: 11783-11790

• PubMed: 33101759 
• DOI: https://doi.org/10.1021/acscatal.0c01619
• Primary Citation Related Structures: 
  6R1L


• PubMed Abstract: 
  

  We present an artificial metalloenzyme based on the transcriptional regulator LmrR that exhibits dynamics involving the positioning of its abiological metal cofactor. The position of the cofactor, in turn, was found to be related to the preferred catalytic reactivity, which is either the enantioselective Friedel-Crafts alkylation of indoles with β-substituted enones or the tandem Friedel-Crafts alkylation/enantioselective protonation of indoles with α-substituted enones. The artificial metalloenzyme could be specialized for one of these catalytic reactions introducing a single mutation in the protein. The relation between cofactor dynamics and activity and selectivity in catalysis has not been described for natural enzymes and, to date, appears to be particular for artificial metalloenzymes.

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Organizational Affiliation: 
• Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193, Cerdanyola del Vallés, Barcelona, Spain.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.01 kDa 
• Atom Count: 861 
• Modeled Residue Count: 100 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, PadR-like family	A	126	Lactococcus cremoris subsp. cremoris MG1363	Mutation(s): 0  Gene Names: llmg_0323
UniProt
Find proteins for A2RI36 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore A2RI36  Go to UniProtKB:  A2RI36

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHN	B [auth A]	1,10-PHENANTHROLINE C12 H8 N2 DGEZNRSVGBDHLK-UHFFFAOYSA-N
CU	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.248 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.851	α = 90
b = 34.851	β = 90
c = 177.469	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Reddem, R., Thunnissen, A.M.W.H.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research	Netherlands	--

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2021-10-13
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy
• Version 1.2: 2024-01-24
  Changes: Data collection, Refinement description