1J8V | pdb_00001j8v

Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme Exo1 in complex with 4'-nitrophenyl 3I-thiolaminaritrioside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.250 (Depositor) 
  • R-Value Work: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1J8V

This is version 2.2 of the entry. See complete history

Literature

Structural basis for broad substrate specificity in higher plant beta-D-glucan glucohydrolases.

Hrmova, M.De Gori, R.Smith, B.J.Fairweather, J.K.Driguez, H.Varghese, J.N.Fincher, G.B.

(2002) Plant Cell 14: 1033-1052

  • DOI: https://doi.org/10.1105/tpc.010442
  • Primary Citation Related Structures: 
    1J8V

  • PubMed Abstract: 

    Family 3 beta-D-glucan glucohydrolases are distributed widely in higher plants. The enzymes catalyze the hydrolytic removal of beta-D-glucosyl residues from nonreducing termini of a range of beta-D-glucans and beta-D-oligoglucosides. Their broad specificity can be explained by x-ray crystallographic data obtained from a barley beta-D-glucan glucohydrolase in complex with nonhydrolyzable S-glycoside substrate analogs and by molecular modeling of enzyme/substrate complexes. The glucosyl residue that occupies binding subsite -1 is locked tightly into a fixed position through extensive hydrogen bonding with six amino acid residues near the bottom of an active site pocket. In contrast, the glucosyl residue at subsite +1 is located between two Trp residues at the entrance of the pocket, where it is constrained less tightly. The relative flexibility of binding at subsite +1, coupled with the projection of the remainder of bound substrate away from the enzyme's surface, means that the overall active site can accommodate a range of substrates with variable spatial dispositions of adjacent beta-D-glucosyl residues. The broad specificity for glycosidic linkage type enables the enzyme to perform diverse functions during plant development.


  • Organizational Affiliation
    • Department of Plant Science, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia.

Macromolecule Content 

  • Total Structure Weight: 68.23 kDa 
  • Atom Count: 4,999 
  • Modeled Residue Count: 602 
  • Deposited Residue Count: 605 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-D-glucan glucohydrolase isoenzyme EXO1605Hordeum vulgareMutation(s): 0 
EC: 3.2.1.58
UniProt
Find proteins for Q9XEI3 (Hordeum vulgare subsp. vulgare)
Explore Q9XEI3 
Go to UniProtKB:  Q9XEI3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XEI3
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G92311HB
GlyCosmos: G92311HB
GlyGen: G92311HB
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LAM

Query on LAM



Download:Ideal Coordinates CCD File
E [auth A]4'-NITROPHENYL-S-(BETA-D-GLUCOPYRANOSYL)-(1-3)-(3-THIO-BETA-D-GLUCOPYRANOSYL)-(1-3)-BETA-D-GLUCOPYRANOSIDE
C24 H35 N O17 S
VWNONHZCCMYIGR-VGNFVTAUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.250 (Depositor) 
  • R-Value Work:  0.201 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.533α = 90
b = 100.533β = 90
c = 181.959γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary