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: light scattering

Macromolecule Content

• Total Structure Weight: 32.99 kDa 
• Atom Count: 2,461 
• Modelled Residue Count: 260 
• Deposited Residue Count: 282 
• Unique protein chains: 1

 6UAW

Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava (PvGH128_II) in complex with laminaritriose

• PDB DOI:  https://doi.org/10.2210/pdb6UAW/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas viridiflava
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-11 Released: 2020-05-20 
• Deposition Author(s): Santos, C.R., Costa, P.A.C.R., Lima, E.A., Mandelli, F., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.192 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

Literature

Structural insights into beta-1,3-glucan cleavage by a glycoside hydrolase family.

Santos, C.R., Costa, P.A.C.R., Vieira, P.S., Gonzalez, S.E.T., Correa, T.L.R., Lima, E.A., Mandelli, F., Pirolla, R.A.S., Domingues, M.N., Cabral, L., Martins, M.P., Cordeiro, R.L., Junior, A.T., Souza, B.P., Prates, E.T., Gozzo, F.C., Persinoti, G.F., Skaf, M.S., Murakami, M.T.

(2020) Nat Chem Biol 16: 920-929

• PubMed: 32451508 
• DOI: https://doi.org/10.1038/s41589-020-0554-5
• Primary Citation of Related Structures:  
  6UAQ, 6UAR, 6UAS, 6UAT, 6UAU, 6UAV, 6UAW, 6UAX, 6UAY, 6UAZ, 6UB0, 6UB1, 6UB2, 6UB3, 6UB4, 6UB5, 6UB6, 6UB7, 6UB8, 6UBA, 6UBB, 6UBC, 6UBD, 6UFL, 6UFZ


• PubMed Abstract: 
  

The fundamental and assorted roles of β-1,3-glucans in nature are underpinned on diverse chemistry and molecular structures, demanding sophisticated and intricate enzymatic systems for their processing. In this work, the selectivity and modes of action of a glycoside hydrolase family active on β-1,3-glucans were systematically investigated combining sequence similarity network, phylogeny, X-ray crystallography, enzyme kinetics, mutagenesis and molecular dynamics. This family exhibits a minimalist and versatile (α/β)-barrel scaffold, which can harbor distinguishing exo or endo modes of action, including an ancillary-binding site for the anchoring of triple-helical β-1,3-glucans. The substrate binding occurs via a hydrophobic knuckle complementary to the canonical curved conformation of β-1,3-glucans or through a substrate conformational change imposed by the active-site topology of some fungal enzymes. Together, these findings expand our understanding of the enzymatic arsenal of bacteria and fungi for the breakdown and modification of β-1,3-glucans, which can be exploited for biotechnological applications.

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Organizational Affiliation: 

Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyco_hydro_cc domain-containing protein	A	282	Pseudomonas viridiflava	Mutation(s): 0  Gene Names: CFBP1590__2373
UniProt
Find proteins for A0A1Y6JJH6 (Pseudomonas viridiflava) Explore A0A1Y6JJH6  Go to UniProtKB:  A0A1Y6JJH6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G00024MO GlyCosmos:  G00024MO GlyGen:  G00024MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.192 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.432	α = 90
b = 33.871	β = 113.11
c = 84.563	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Santos, C.R., Costa, P.A.C.R., Lima, E.A., Mandelli, F., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	15/26982-0

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-08-05
  Changes: Database references