6L2D

Crystal structure of a cupin protein (tm1459) in copper (Cu) substituted form

• PDB DOI: https://doi.org/10.2210/pdb6L2D/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-03 Released: 2020-04-01 
• Deposition Author(s): Fujieda, N., Ichihashi, H., Nishikawa, Y., Kurisu, G., Itoh, S.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.186 
• R-Value Work: 0.151 
• R-Value Observed: 0.151 

Literature

Cupin Variants as a Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes.

Fujieda, N., Ichihashi, H., Yuasa, M., Nishikawa, Y., Kurisu, G., Itoh, S.

(2020) Angew Chem Int Ed Engl 59: 7717-7720

• PubMed: 32073197 
• DOI: https://doi.org/10.1002/anie.202000129
• Primary Citation of Related Structures:  
  6L2D, 6L2E, 6L2F


• PubMed Abstract: 
  

  Cupin superfamily proteins (TM1459) work as a macromolecular ligand framework with a double-stranded β-barrel structure ligating to a Cu ion through histidine side chains. Variegating the first coordination sphere of TM1459 revealed that H52A and H54A/H58A mutants effectively catalyzed the diastereo- and enantioselective Michael addition reaction of nitroalkanes to an α,β-unsaturated ketone. Moreover, calculated substrate docking signified C106N and F104W single-point mutations, which inverted the diastereoselectivity of H52A and further improved the stereoselectivity of H54A/H58A, respectively.

---

Organizational Affiliation: 

Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka, 599-8531, Japan.

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: 27.05 kDa 
• Atom Count: 2,153 
• Modelled Residue Count: 232 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin_2 domain-containing protein	A, B	118	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM_1459
UniProt
Find proteins for Q9X1H0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1H0  Go to UniProtKB:  Q9X1H0

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.186 
• R-Value Work: 0.151 
• R-Value Observed: 0.151 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.521	α = 90
b = 57.808	β = 90
c = 74.963	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
SHELX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Fujieda, N., Ichihashi, H., Nishikawa, Y., Kurisu, G., Itoh, S.

---

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	16H01025
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18H04270

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description