7JVI | pdb_00007jvi

Crystal structure of a beta-helix domain retrieved from capybara gut metagenome

• PDB DOI: https://doi.org/10.2210/pdb7JVI/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): metagenome
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-21 Released: 2021-09-08 
• Deposition Author(s): Martins, M.P., Genoroso, W.C., Domingues, M.N., Persinoti, G.F., Morais, M.A.B., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.213 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides.

Cabral, L., Persinoti, G.F., Paixao, D.A.A., Martins, M.P., Morais, M.A.B., Chinaglia, M., Domingues, M.N., Sforca, M.L., Pirolla, R.A.S., Generoso, W.C., Santos, C.A., Maciel, L.F., Terrapon, N., Lombard, V., Henrissat, B., Murakami, M.T.

(2022) Nat Commun 13: 629-629

• PubMed: 35110564 
• DOI: https://doi.org/10.1038/s41467-022-28310-y
• Primary Citation Related Structures: 
  7JVI


• PubMed Abstract: 
  

  The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy.

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Organizational Affiliation: 
• Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil. [e-mail].
Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.
Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France.
Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.
Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: SAXS

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 186.9 kDa 
• Atom Count: 6,979 
• Modeled Residue Count: 842 
• Deposited Residue Count: 1,694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-helix domain	A, B	847	metagenome	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.213 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.979	α = 90
b = 144.507	β = 90
c = 169.492	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
SHELXDE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-08 
Deposition Author(s): Martins, M.P., Genoroso, W.C., Domingues, M.N., Persinoti, G.F., Morais, M.A.B., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/26982-0
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	306135/2016-7
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	408600/2018-7
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	439195/2016-02018-7
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	142332/2017-8

Revision History  

• Version 1.0: 2021-09-08
  Type: Initial release
  
• Version 1.1: 2022-03-30
  Changes: Database references
• Version 1.2: 2024-05-22
  Changes: Data collection