5FOO | pdb_00005foo

6-phospho-beta-glucosidase

PDB DOI: https://doi.org/10.2210/pdb5FOO/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pyogenes M1 GAS
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-11-24 Released: 2016-02-17
Deposition Author(s): Jin, Y., Kwan, D.H., Withers, S.G., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Chemoenzymatic Synthesis of 6-Phospho-Cyclophellitol as a Novel Probe of 6-Phospho-Beta-Glucosidases.

Kwan, D.H., Jin, Y., Jiang, J., Chen, H., Kotzler, M.P., Overkleeft, H.S., Davies, G.J., Withers, S.G.

(2016) FEBS Lett 590: 461

PubMed: 26790390 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12059
Primary Citation of Related Structures:
5FOO

PubMed Abstract:
Covalent, mechanism-based inhibitors of glycosidases are valuable probe molecules for visualizing enzyme activities in complex systems. We, here, describe the chemoenzymatic synthesis of 6-phospho-cyclophellitol and evaluate its behaviour as a mechanism-based inactivator of the Streptococcus pyogenes 6-phospho-β-glucosidase from CAZy family GH1. We further present the three-dimensional structure of the inactivated enzyme, which reveals the constellation of active site residues responsible for the enzyme's specificity and confirms the covalent nature of the inactivation.

Organizational Affiliation

Department of Chemistry, University of British Columbia, BC, Canada.

Macromolecule Content

Total Structure Weight: 334.54 kDa
Atom Count: 23,838
Modelled Residue Count: 2,777
Deposited Residue Count: 2,880
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-PHOSPHO-BETA-D GLYCOSIDASE	A, B, C, D, E A, B, C, D, E, F	480	Streptococcus pyogenes M1 GAS	Mutation(s): 1 EC: 3.2.1.21 (PDB Primary Data), 3.2.1.86 (PDB Primary Data)
UniProt
Find proteins for Q99YP9 (Streptococcus pyogenes serotype M1) Explore Q99YP9 Go to UniProtKB: Q99YP9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99YP9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JAZ Query on JAZ Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain G [auth A] SDF format, chain IA [auth E] SDF format, chain LA [auth F] SDF format, chain O [auth B] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain LA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain W [auth C]	BA [auth D] G [auth A] IA [auth E] LA [auth F] O [auth B] BA [auth D], G [auth A], IA [auth E], LA [auth F], O [auth B], W [auth C]	6-PHOSPHOCYCLOPHELLITOL C₇ H₁₅ O₉ P UJSILGAUEGUBGA-NYLBLOMBSA-N		Interactions Focus chain BA [auth D] Focus chain G [auth A] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain O [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain G [auth A] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain O [auth B] Focus chain W [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C] mmCIF format, chain X [auth C]	X [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain KA [auth E] SDF format, chain M [auth A] SDF format, chain OA [auth F] SDF format, chain U [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain U [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain KA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain U [auth B]	AA [auth C] GA [auth D] KA [auth E] M [auth A] OA [auth F] AA [auth C], GA [auth D], KA [auth E], M [auth A], OA [auth F], U [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain KA [auth E] Focus chain M [auth A] Focus chain OA [auth F] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain KA [auth E] Focus chain M [auth A] Focus chain OA [auth F] Focus chain U [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	CA [auth D] DA [auth D] EA [auth D] FA [auth D] H [auth A] CA [auth D], DA [auth D], EA [auth D], FA [auth D], H [auth A], I [auth A], J [auth A], JA [auth E], K [auth A], L [auth A], MA [auth F], NA [auth F], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain N [auth A] SDF format, chain V [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] mmCIF format, chain HA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B]	HA [auth D], N [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth D] Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain HA [auth D] Focus chain N [auth A] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.174 (Depositor), 0.180 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.017	α = 90
b = 109.899	β = 92.02
c = 158.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-17
Type: Initial release
Version 1.1: 2016-03-02
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary