6Z1H | pdb_00006z1h

Ancestral glycosidase (family 1)

• PDB DOI: https://doi.org/10.2210/pdb6Z1H/pdb

• Classification: HYDROLASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-13 Released: 2020-07-22 
• Deposition Author(s): Gavira, J.A., Risso, V.A., Sanchez-Ruiz, J.M., Gamiz-Arco, G., Gutierrez-Rus, L., Ibarra-Molero, B., Hoshino, Y., Petrovic, D., Romero-Rivera, A., Seelig, B., Kamerlin, S.C.L., Gaucher, E.A.
• Funding Organization(s): Human Frontier Science Program (HFSP), Spanish Ministry of Science, Innovation, and Universities

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase.

Gamiz-Arco, G., Gutierrez-Rus, L.I., Risso, V.A., Ibarra-Molero, B., Hoshino, Y., Petrovic, D., Justicia, J., Cuerva, J.M., Romero-Rivera, A., Seelig, B., Gavira, J.A., Kamerlin, S.C.L., Gaucher, E.A., Sanchez-Ruiz, J.M.

(2021) Nat Commun 12: 380-380

• PubMed: 33452262 
• DOI: https://doi.org/10.1038/s41467-020-20630-1
• Primary Citation Related Structures: 
  6Z1H, 6Z1M


• PubMed Abstract: 
  

  Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.

---

Organizational Affiliation: 
• Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain.
Department of Biology, Georgia State University, Atlanta, GA, 30303, USA.
Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden.
Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, 431 50, Gothenburg, Sweden.
Departamento de Quimica Organica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain.
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America, & BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Avenida de las Palmeras 4, Granada, 18100, Armilla, Spain.
Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden. [e-mail].
Department of Biology, Georgia State University, Atlanta, GA, 30303, USA. [e-mail].
Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Macromolecule Content 

• Total Structure Weight: 108.24 kDa 
• Atom Count: 6,593 
• Modeled Residue Count: 786 
• Deposited Residue Count: 949 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANCESTRAL RECONSTRUCTED GLYCOSIDASE	A, B	459	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Residues 249 to 266 of chain A and 246 to 258 of chain B could not be identified and has been included as UNK in chain C and D, respectively.	C	18	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Residues 249 to 266 of chain A and 246 to 258 of chain B could not be identified and has been included as UNK in chain C and D, respectively.	D	13	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	G [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.263	α = 90
b = 80.668	β = 100.061
c = 97.808	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Gavira, J.A., Risso, V.A., Sanchez-Ruiz, J.M., Gamiz-Arco, G., Gutierrez-Rus, L., Ibarra-Molero, B., Hoshino, Y., Petrovic, D., Romero-Rivera, A., Seelig, B., Kamerlin, S.C.L., Gaucher, E.A.

---

Funding Organization	Location	Grant Number
Human Frontier Science Program (HFSP)	United States	RGP0041/2017
Spanish Ministry of Science, Innovation, and Universities	Spain	BIO2016-74875-P

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references, Structure summary
• Version 1.2: 2021-01-27
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description