6HMH

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine) and alpha-1,2-mannobiose

PDB DOI: https://doi.org/10.2210/pdb6HMH/pdb

Classification: HYDROLASE
Organism(s): Bacteroides xylanisolvens XB1A
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-09-12 Released: 2018-09-26
Deposition Author(s): Sobala, L.F., Lu, D., Zhu, S., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Sollogoub, M., Jimenez-Barbero, J., Davies, G.J.
Funding Organization(s): European Research Council, Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free: 0.139
R-Value Work: 0.124
R-Value Observed: 0.125

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

From 1,4-Disaccharide to 1,3-Glycosyl Carbasugar: Synthesis of a Bespoke Inhibitor of Family GH99 Endo-alpha-mannosidase.

Lu, D., Zhu, S., Sobala, L.F., Bernardo-Seisdedos, G., Millet, O., Zhang, Y., Jimenez-Barbero, J., Davies, G.J., Sollogoub, M.

(2018) Org Lett 20: 7488-7492

PubMed: 30427198 Search on PubMed
DOI: https://doi.org/10.1021/acs.orglett.8b03260
Primary Citation of Related Structures:
6HMG, 6HMH

PubMed Abstract:
Understanding the enzyme reaction mechanism can lead to the design of enzyme inhibitors. A Claisen rearrangement was used to allow conversion of an α-1,4-disaccharide into an α-1,3-linked glycosyl carbasugar to target the endo-α-mannosidase from the GH99 glycosidase family, which, unusually, is believed to act through a 1,2-anhydrosugar "epoxide" intermediate. Using NMR and X-ray crystallography, it is shown that glucosyl carbasugar α-aziridines can act as reasonably potent endo-α-mannosidase inhibitors, likely by virtue of their shape mimicry and the interactions of the aziridine nitrogen with the conserved catalytic acid/base of the enzyme active site.

Organizational Affiliation

Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France.

Macromolecule Content

Total Structure Weight: 44.67 kDa
Atom Count: 3,512
Modelled Residue Count: 341
Deposited Residue Count: 385
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 71	A	385	Bacteroides xylanisolvens XB1A	Mutation(s): 0 Gene Names: BXY_34140
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Explore D6D1V7 Go to UniProtKB: D6D1V7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D6D1V7
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G53402KW GlyCosmos: G53402KW GlyGen: G53402KW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GDQ (Subject of Investigation/LOI) Query on GDQ Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	(1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol C₇ H₁₃ N O₃ JACJTGDBUDQHPY-VOQCIKJUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111 Query on PRD_900111	B	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free: 0.139
R-Value Work: 0.124
R-Value Observed: 0.125
Space Group: I 4
Diffraction Data: https://doi.org/10.5281/zenodo.4431701

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.175	α = 90
b = 108.175	β = 90
c = 67.575	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-09-26

Deposition Author(s):

Sobala, L.F.

Lu, D.

Zhu, S.

Bernardo-Seisdedos, G.

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	322942
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2017-85496-P
Spanish Ministry of Economy and Competitiveness	Spain	CTQ2015-64597-C2-1P

Revision History (Full details and data files)

Version 1.0: 2018-09-26
Type: Initial release
Version 1.1: 2018-11-28
Changes: Data collection, Database references
Version 2.0: 2018-12-19
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2019-04-24
Changes: Data collection, Database references
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 3.2: 2024-01-24
Changes: Data collection, Database references, Refinement description