2ZOX

Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase

Noguchi, J.Hayashi, Y.Baba, Y.Okino, N.Kimura, M.Ito, M.Kakuta, Y.

(2008) Biochem Biophys Res Commun 374: 549-552

  • DOI: https://doi.org/10.1016/j.bbrc.2008.07.089
  • Primary Citation of Related Structures:  
    2ZOX

  • PubMed Abstract: 

    Human cytosolic beta-glucosidase, also known as klotho-related protein (KLrP, GBA3), is an enzyme that hydrolyzes various beta-D-glucosides, including glucosylceramide. We recently reported the crystal structure of KLrP in complex with glucose [Y. Hayashi, N. Okino, Y. Kakuta, T. Shikanai, M. Tani, H. Narimatsu, M. Ito, Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase, J. Biol. Chem. 282 (2007) 30889-30900]. Here, we report the crystal structure of a covalent intermediate of the KLrP mutant E165Q, in which glucose was covalently bound to a nucleophile, Glu(373). The structure confirms the double displacement mechanism of the retaining beta-glucosidase. In addition, the structure suggests that a water molecule could be involved in the stabilization of transition states through a sugar, 2-hydroxyl.


  • Organizational Affiliation

    Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8581, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosolic beta-glucosidase469Homo sapiensMutation(s): 1 
Gene Names: GBA3CBGCBGL1
EC: 3.2.1.21 (PDB Primary Data), 3.2.1.46 (UniProt), 3.2.1.45 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H227 (Homo sapiens)
Explore Q9H227 
Go to UniProtKB:  Q9H227
PHAROS:  Q9H227
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H227
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNG
Query on PNG

Download Ideal Coordinates CCD File 
C [auth A]4-nitrophenyl alpha-D-glucopyranoside
C12 H15 N O8
IFBHRQDFSNCLOZ-ZIQFBCGOSA-N
OLA
Query on OLA

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H [auth A]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PLM
Query on PLM

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G [auth A],
I [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
GLC
Query on GLC

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B [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
PO4
Query on PO4

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F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

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D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.12α = 90
b = 82.529β = 90
c = 91.673γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.3: 2021-11-10
    Changes: Database references, Structure summary
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Structure summary