8VA3 | pdb_00008va3

Crystal structure of CapGH3b enzyme retrieved from capybara gut metagenome

PDB DOI: https://doi.org/10.2210/pdb8VA3/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-11 Released: 2024-10-23
Deposition Author(s): Martins, M.P., Morais, M.A.B., Chinaglia, M., Mandelli, F., Lima, E.A., Murakami, M.T.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.187 (Depositor), 0.187 (DCC)
R-Value Work:
0.155 (Depositor), 0.155 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A functionally augmented carbohydrate utilization locus from herbivore gut microbiota fueled by dietary beta-glucans.

Mandelli, F., Martins, M.P., Chinaglia, M., Lima, E.A., Morais, M.A.B., Lima, T.B., Cabral, L., Pirolla, R.A.S., Fuzita, F.J., Paixao, D.A.A., Andrade, M.O., Wolf, L.D., Vieira, P.S., Persinoti, G.F., Murakami, M.T.

(2024) NPJ Biofilms Microbiomes 10: 105-105

PubMed: 39397008 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41522-024-00578-6
Primary Citation Related Structures:
8VA3, 8VA4, 8VA7

PubMed Abstract:
Gut microbiota members from the Bacteroidota phylum play a pivotal role in mammalian health and metabolism. They thrive in this diverse ecosystem due to their notable ability to cope with distinct recalcitrant dietary glycans via polysaccharide utilization loci (PULs). Our study reveals that a PUL from an herbivore gut bacterium belonging to the Bacteroidota phylum, with a gene composition similar to that in the human gut, exhibits extended functionality. While the human gut PUL targets mixed-linkage β-glucans specifically, the herbivore gut PUL also efficiently processes linear and substituted β-1,3-glucans. This gain of function emerges from molecular adaptations in recognition proteins and carbohydrate-active enzymes, including a β-glucosidase specialized for β(1,6)-glucosyl linkages, a typical substitution in β(1,3)-glucans. These findings broaden the existing model for non-cellulosic β-glucans utilization by gut bacteria, revealing an additional layer of functional and evolutionary complexity within the gut microbiota, beyond conventional gene insertions/deletions to intricate biochemical interactions.

Organizational Affiliation

Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil.

Macromolecule Content

Total Structure Weight: 176.26 kDa
Atom Count: 13,446
Modeled Residue Count: 1,515
Deposited Residue Count: 1,560
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 3	A, B	780	metagenome	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain X [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain X [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain X [auth B] mmCIF format, chain E [auth A]	D [auth A], E [auth A], X [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain X [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain X [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain W [auth B] MOL2 format, chain C [auth A] MOL2 format, chain W [auth B] mmCIF format, chain C [auth A] mmCIF format, chain W [auth B]	C [auth A], W [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain W [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] MOL2 format, chain JA [auth B] mmCIF format, chain JA [auth B]	JA [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain JA [auth B] Interactions & Density Focus chain JA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain O [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain HA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain O [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain O [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain IA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain IA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain IA [auth B]	IA [auth B], T [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain T [auth A] Interactions & Density Focus chain IA [auth B] Focus chain T [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]