6YQH

GH146 beta-L-arabinofuranosidase bound to covalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.129 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.

McGregor, N.G.S.Coines, J.Borlandelli, V.Amaki, S.Artola, M.Nin-Hill, A.Linzel, D.Yamada, C.Arakawa, T.Ishiwata, A.Ito, Y.van der Marel, G.A.Codee, J.D.C.Fushinobu, S.Overkleeft, H.S.Rovira, C.Davies, G.J.

(2021) Angew Chem Int Ed Engl 60: 5754-5758

  • DOI: 10.1002/anie.202013920
  • Primary Citation of Related Structures:  
    6YQH, 7BZL, 7DIF

  • PubMed Abstract: 
  • The recent discovery of zinc-dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys) 3 (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on a Zn-coordinated cysteine nucleophile and passing through a thioglycosyl enzyme intermediate, remains controversial ...

    The recent discovery of zinc-dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys) 3 (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on a Zn-coordinated cysteine nucleophile and passing through a thioglycosyl enzyme intermediate, remains controversial. This is primarily due to the expected stability of the intermediate C-S bond. To facilitate the study of this atypical mechanism, we report the synthesis of a cyclophellitol-derived β-l-arabinofuranosidase inhibitor, hypothesised to react with the catalytic nucleophile to form a non-hydrolysable adduct analogous to the mechanistic covalent intermediate. This β-l-arabinofuranosidase inhibitor reacts exclusively with the proposed cysteine thiol catalytic nucleophiles of representatives of GH families 127 and 146. X-ray crystal structures determined for the resulting adducts enable MD and QM/MM simulations, which provide insight into the mechanism of thioglycosyl enzyme intermediate breakdown. Leveraging the unique chemistry of cyclophellitol derivatives, the structures and simulations presented here support the assignment of a zinc-coordinated cysteine as the catalytic nucleophile and illuminate the finely tuned energetics of this remarkable metalloenzyme clan.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetyl-CoA carboxylase, biotin carboxylase AAA802Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_0349
Find proteins for Q8AAW3 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Explore Q8AAW3 
Go to UniProtKB:  Q8AAW3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
AAA
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
AAA
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PJ5
Query on PJ5

Download Ideal Coordinates CCD File 
AAA
(1~{S},2~{S},3~{S},4~{S})-4-(hydroxymethyl)cyclopentane-1,2,3-triol
C6 H12 O4
PHKHGSSZAJVEQK-BXKVDMCESA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AAA
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AAA
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
AAA
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.129 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.418α = 90
b = 95.418β = 90
c = 189.068γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R001162/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2021-03-10
    Changes: Database references