6UBA

Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI) in complex with laminaritriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


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

  • DOI: 10.1038/s41589-020-0554-5
  • Primary Citation of Related Structures:  
    6UAZ, 6UBB, 6UBA, 6UAS, 6UB4, 6UAR, 6UB3, 6UAU, 6UB6, 6UAT

  • 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 ...

    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.


    Organizational Affiliation

    Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil. mario.murakami@lnbr.cnpem.br.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyco_hydro_cc domain-containing proteinABCDEFGHABCDEFGHIJ
266Aureobasidium namibiae CBS 147.97Mutation(s): 0 
Gene Names: M436DRAFT_66913
Find proteins for A0A074W9U7 (Aureobasidium namibiae CBS 147.97)
Explore A0A074W9U7 
Go to UniProtKB:  A0A074W9U7
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose
K, M, O, Q, U, W, Y, a, c
3 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose
L, N, P, R, S, T, V, X, Z, b, d
2 N/A Oligosaccharides Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900024
Query on PRD_900024
L, N, P, R, S, T, V, X, Z, b, dbeta-laminaribioseOligosaccharide /  Antimicrobial

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.262α = 90
b = 152.798β = 90
c = 169.423γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil15/26982-0

Revision History  (Full details and data files)

  • 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