6Z1M

Structure of an Ancestral glycosidase (family 1) bound to heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1038/s41467-020-20630-1
  • Primary Citation of 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 ...

    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.


    Related Citations: 
    • Novel heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase
      Gamiz-Arco, G., Gutierrez-Rus, L., Risso, V.A., Ibarra-Molero, B., Oshino, Y., Petrovic, D., Romero-Rivera, A., Seelig, B., Gavira, J.A., Kamerlin, S.C.L., Gaucher, E.A., Sanchez-Ruiz, J.M.
      (2020) Biorxiv --: --

    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. sanchezr@ugr.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ancestral reconstructed glycosidaseA, B, C459synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
Q [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
L [auth B],
M [auth B],
R [auth C],
E [auth A],
F [auth A],
L [auth B],
M [auth B],
R [auth C],
S [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
T [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.934α = 90
b = 89.496β = 94.211
c = 141.12γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Human Frontier Science Program (HFSP)United StatesRGP0041/2017
Spanish Ministry of Science, Innovation, and UniversitiesSpainBIO2016-74875-P

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references, Derived calculations