2ZOX | pdb_00002zox

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 (Depositor), 0.205 (DCC)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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 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
Modeled Residue Count: 466
Deposited Residue Count: 469
Unique protein chains: 1

Macromolecules

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| 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 (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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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] mmCIF 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] mmCIF format, chain I [auth A] mmCIF 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] mmCIF 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] mmCIF 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] mmCIF 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 E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [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 (Depositor), 0.205 (DCC)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.192 (Depositor)

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

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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
Version 1.5: 2024-10-30
Changes: Structure summary