5MEH | pdb_00005meh

Crystal structure of alpha-1,2-mannosidase from Caulobacter K31 strain in complex with 1-deoxymannojirimycin

PDB DOI: https://doi.org/10.2210/pdb5MEH/pdb

Classification: HYDROLASE
Organism(s): Caulobacter sp. K31
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2016-11-14 Released: 2016-12-21
Deposition Author(s): Males, A., Davies, G.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.95 Å
R-Value Free:
0.103 (Depositor), 0.103 (DCC)
R-Value Work:
0.091 (Depositor), 0.091 (DCC)
R-Value Observed:
0.092 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Conformational Behaviour of Azasugars Based on Mannuronic Acid.

van Rijssel, E.R., Janssen, A.P.A., Males, A., Davies, G.J., van der Marel, G.A., Overkleeft, H.S., Codee, J.D.C.

(2017) Chembiochem 18: 1297-1304

PubMed: 28256791 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201700080
Primary Citation Related Structures:
5MEH

PubMed Abstract:
A set of mannuronic-acid-based iminosugars, consisting of the C-5-carboxylic acid, methyl ester and amide analogues of 1deoxymannorjirimicin (DMJ), was synthesised and their pH-dependent conformational behaviour was studied. Under acidic conditions the methyl ester and the carboxylic acid adopted an "inverted" ¹ C ₄ chair conformation as opposed to the "normal" ⁴ C ₁ chair at basic pH. This conformational change is explained in terms of the stereoelectronic effects of the ring substituents and it parallels the behaviour of the mannuronic acid ester oxocarbenium ion. Because of this solution-phase behaviour, the mannuronic acid ester azasugar was examined as an inhibitor for a Caulobacter GH47 mannosidase that hydrolyses its substrates by way of a reaction itinerary that proceeds through a ³ H ₄ transition state. No binding was observed for the mannuronic acid ester azasugar, but sub-atomic resolution data were obtained for the DMJ⋅CkGH47 complex, showing two conformations- ³ S ₁ and ¹ C ₄ -for the DMJ inhibitor.

Organizational Affiliation

Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.

Macromolecule Content

Total Structure Weight: 51.06 kDa
Atom Count: 4,229
Modeled Residue Count: 438
Deposited Residue Count: 447
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannosyl-oligosaccharide 1,2-alpha-mannosidase	A	447	Caulobacter sp. K31	Mutation(s): 0 Gene Names: Caul_4035 EC: 3.2.1.113
UniProt
Find proteins for B0SWV2 (Caulobacter sp. (strain K31)) Explore B0SWV2 Go to UniProtKB: B0SWV2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0SWV2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMJ Query on DMJ Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1-DEOXYMANNOJIRIMYCIN C₆ H₁₃ N O₄ LXBIFEVIBLOUGU-KVTDHHQDSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CA Query on CA 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] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.95 Å
R-Value Free: 0.103 (Depositor), 0.103 (DCC)
R-Value Work: 0.091 (Depositor), 0.091 (DCC)
R-Value Observed: 0.092 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.371	α = 90
b = 145.371	β = 90
c = 50.838	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-12-21

Deposition Author(s):

Males, A.

Davies, G.J.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2016-12-21
Type: Initial release
Version 1.1: 2017-03-15
Changes: Database references
Version 1.2: 2017-04-26
Changes: Database references
Version 1.3: 2017-07-12
Changes: Database references
Version 1.4: 2017-08-30
Changes: Author supporting evidence
Version 1.5: 2024-05-08
Changes: Data collection, Database references, Derived calculations