2JJB | pdb_00002jjb

Family 37 trehalase from Escherichia coli in complex with casuarine-6- O-alpha-glucopyranose

PDB DOI: https://doi.org/10.2210/pdb2JJB/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-03-28 Released: 2009-01-13
Deposition Author(s): Gloster, T.M., Roberts, S., Davies, G.J., Cardona, F., Parmeggiani, C., Bonaccini, C., Gratteri, P., Sim, L., Rose, D.R., Goti, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Total Syntheses of Casuarine and its 6-O-Alpha-Glucoside: Complementary Inhibition Towards Glycoside Hydrolases of the Gh31 and Gh37 Families.

Cardona, F., Parmeggiani, C., Faggi, E., Bonaccini, C., Gratteri, P., Sim, L., Gloster, T.M., Roberts, S., Davies, G.J., Rose, D.R., Goti, A.

(2009) Chemistry 15: 1627

PubMed: 19123216 Search on PubMed
DOI: https://doi.org/10.1002/chem.200801578
Primary Citation Related Structures:
2JJB, 3CTT

PubMed Abstract:
Total synthesis of naturally occurring casuarine (1) and the first total synthesis of casuarine 6-O-alpha-glucoside (2) were achieved through complete stereoselective nitrone cycloaddition, Tamao-Fleming oxidation and selective alpha-glucosylation as key steps. Biological assays of the two compounds proved their strong and selective inhibitory properties towards glucoamylase NtMGAM and trehalase Tre37A, respectively, which place them among the most powerful inhibitors of these enzymes. The structural determination of the complexes of NtMGAM with 1 and of Tre37A with 2 revealed interesting similarities in the catalytic sites of these two enzymes which belong to different families and clans.

Organizational Affiliation

Department of Organic Chemistry U. Schiff, Laboratory of Design, Synthesis and Study of Biologically Active Heterocycles, University of Florence, Via della Lastruccia, 13, 50019 Sesto Fiorentino (FI), Italy.

Macromolecule Content

Total Structure Weight: 247.48 kDa
Atom Count: 18,411
Modeled Residue Count: 1,997
Deposited Residue Count: 2,140
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC TREHALASE	A, B, C, D	535	Escherichia coli K-12	Mutation(s): 0 EC: 3.2.1.28
UniProt
Find proteins for P13482 (Escherichia coli (strain K12)) Explore P13482 Go to UniProtKB: P13482
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13482
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3CU Query on 3CU Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain RA [auth D] SDF format, chain T [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain T [auth B]	DA [auth C], E [auth A], RA [auth D], T [auth B]	CASUARINE C₈ H₁₅ N O₅ AXTGOJVKRHFYBT-XAZAIFFQSA-N		Interactions Focus chain DA [auth C] Focus chain E [auth A] Focus chain RA [auth D] Focus chain T [auth B] Interactions & Density Focus chain DA [auth C] Focus chain E [auth A] Focus chain RA [auth D] Focus chain T [auth B]
GLC Query on GLC Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain SA [auth D] SDF format, chain U [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain U [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain U [auth B]	EA [auth C], F [auth A], SA [auth D], U [auth B]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain EA [auth C] Focus chain F [auth A] Focus chain SA [auth D] Focus chain U [auth B] Interactions & Density Focus chain EA [auth C] Focus chain F [auth A] Focus chain SA [auth D] Focus chain U [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain FA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] SDF format, chain MA [auth C] SDF format, chain GA [auth C] SDF format, chain G [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain MA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A]	AA [auth B] AB [auth D] BA [auth B] FA [auth C] G [auth A] AA [auth B], AB [auth D], BA [auth B], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], R [auth A], TA [auth D], UA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain QA [auth C] SDF format, chain S [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain S [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain S [auth A]	CA [auth B], QA [auth C], S [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain QA [auth C] Focus chain S [auth A] Interactions & Density Focus chain CA [auth B] Focus chain QA [auth C] Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.224 (Depositor), 0.224 (DCC)
R-Value Work: 0.177 (Depositor), 0.177 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.481	α = 90
b = 117.863	β = 90
c = 203.451	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-01-13
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2024-11-20
Changes: Structure summary