7BTK | pdb_00007btk

E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA01

• PDB DOI: https://doi.org/10.2210/pdb7BTK/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-04-01 Released: 2021-03-03 
• Deposition Author(s): Chen, X., Hu, Y.L., Liu, Q.M., Gao, Y., Yuan, R., Guo, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.233 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Two-Dimensional Design Strategy to Construct Smart Fluorescent Probes for the Precise Tracking of Senescence.

Gao, Y., Hu, Y., Liu, Q., Li, X., Li, X., Kim, C.Y., James, T.D., Li, J., Chen, X., Guo, Y.

(2021) Angew Chem Int Ed Engl 60: 10756-10765

• PubMed: 33624914 
• DOI: https://doi.org/10.1002/anie.202101278
• Primary Citation Related Structures: 
  7BRS, 7BTK


• PubMed Abstract: 
  

  The tracking of cellular senescence usually depends on the detection of senescence-associated β-galactosidase (SA-β-gal). Previous probes for SA-β-gal with this purpose only cover a single dimension: the accumulation of this enzyme in lysosomes. However, this is insufficient to determine the destiny of senescence because endogenous β-gal enriched in lysosomes is not only related to senescence, but also to some other physiological processes. To address this issue, we introduce our fluorescent probes including a second dimension: lysosomal pH, since de-acidification is a unique feature of the lysosomes in senescent cells. With this novel design, our probes achieved excellent discrimination of SA-β-gal from cancer-associated β-gal, which enables them to track cellular senescence as well as tissue aging more precisely. Our crystal structures of a model enzyme E. coli β-gal mutant (E537Q) complexed with each probe further revealed the structural basis for probe recognition.

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Organizational Affiliation: 
• Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, China.
State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, 79968, USA.
Department of Chemistry, University of Bath, Bath, BA2 7AY, UK.
Clinical Medicine Scientific and Technical Innovation Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200092, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 472.39 kDa 
• Atom Count: 33,869 
• Modeled Residue Count: 4,086 
• Deposited Residue Count: 4,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	1,025	Escherichia coli K-12	Mutation(s): 1  Gene Names: lacZ EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12)) Explore P00722  Go to UniProtKB:  P00722

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F6L (Subject of Investigation/LOI)	E [auth A], JA [auth C], V [auth B], WA [auth D]	4-[[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-2H-indol-1-yl]methyl]benzoic acid C32 H34 N O8 ZRXNUVMWWIBYNP-BARJCIPKSA-O
GOL	IA [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	AA [auth B], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HA [auth B], HB [auth D], IB [auth D], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], VA [auth C], Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	F [auth A], G [auth A], KA [auth C], LA [auth C], W [auth B], XA [auth D], YA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	AB [auth D], H [auth A], I [auth A], MA [auth C], NA [auth C], X [auth B], ZA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.233 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 249.832	α = 90
b = 85.454	β = 94.15
c = 243.307	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Chen, X., Hu, Y.L., Liu, Q.M., Gao, Y., Yuan, R., Guo, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21977082
National Natural Science Foundation of China (NSFC)	China	21472148
National Natural Science Foundation of China (NSFC)	China	21807088
National Natural Science Foundation of China (NSFC)	China	81872747

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 1.2: 2021-05-12
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Database references, Refinement description