2ZOX

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

PDB DOI: https://doi.org/10.2210/pdb2ZOX/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-06-17 Released: 2008-09-30
Deposition Author(s): Noguchi, J., Hayashi, Y., Baba, Y., Okino, N., Kimura, M., Ito, M., Kakuta, Y.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 18662675 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 55.26 kDa
Atom Count: 4,092
Modelled Residue Count: 466
Deposited Residue Count: 469
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosolic beta-glucosidase	A	469	Homo sapiens	Mutation(s): 1 Gene Names: GBA3, CBG, CBGL1 EC: 3.2.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H227 (Homo sapiens) Explore Q9H227 Go to UniProtKB: Q9H227
PHAROS: Q9H227
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H227
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PNG Query on PNG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	4-nitrophenyl alpha-D-glucopyranoside C₁₂ H₁₅ N O₈ IFBHRQDFSNCLOZ-ZIQFBCGOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
OLA Query on OLA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A]	G [auth A], I [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain I [auth A]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

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 = 66.12	α = 90
b = 82.529	β = 90
c = 91.673	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-30

Deposition Author(s):

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