3GBE | pdb_00003gbe

Crystal structure of the isomaltulose synthase SmuA from Protaminobacter rubrum in complex with the inhibitor deoxynojirimycin

PDB DOI: https://doi.org/10.2210/pdb3GBE/pdb

Classification: ISOMERASE
Organism(s): Serratia plymuthica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-19 Released: 2009-05-26
Deposition Author(s): Ravaud, S., Robert, X., Haser, R., Aghajari, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.197 (Depositor), 0.189 (DCC)
R-Value Work:
0.171 (Depositor), 0.165 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural determinants of product specificity of sucrose isomerases

Ravaud, S., Robert, X., Watzlawick, H., Haser, R., Mattes, R., Aghajari, N.

(2009) FEBS Lett 583: 1964-1968

PubMed: 19427862 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2009.05.002
Primary Citation Related Structures:
3GBD, 3GBE

PubMed Abstract:
The healthy sweetener isomaltulose is industrially produced from the conversion of sucrose by the sucrose isomerase SmuA from Protaminobacter rubrum. Crystal structures of SmuA in native and deoxynojirimycin complexed forms completed with modeling studies unravel the characteristics of the isomaltulose synthases catalytic pocket and their substrate binding mode. Comparison with the trehalulose synthase MutB highlights the role of Arg(298) and Arg(306) active site residues and surface charges in controlling product specificity of sucrose isomerases (isomaltulose versus trehalulose). The results provide a rationale for the specific design of optimized enzymes.

Organizational Affiliation

Institut de Biologie et Chimie des Protéines, UMR 5086-CNRS/Université de Lyon, IFR128 BioSciences Gerland-Lyon Sud, Lyon, France.

Macromolecule Content

Total Structure Weight: 66.54 kDa
Atom Count: 5,452
Modeled Residue Count: 558
Deposited Residue Count: 558
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose isomerase SmuA from Protaminobacter rubrum	A	558	Serratia plymuthica	Mutation(s): 0 Gene Names: smuA EC: 5.4.99.11
UniProt
Find proteins for D0VX20 (Serratia plymuthica) Explore D0VX20 Go to UniProtKB: D0VX20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC 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]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NOJ Query on NOJ Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	1-DEOXYNOJIRIMYCIN C₆ H₁₃ N O₄ LXBIFEVIBLOUGU-JGWLITMVSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.197 (Depositor), 0.189 (DCC)
R-Value Work: 0.171 (Depositor), 0.165 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.9	α = 90
b = 80.4	β = 90
c = 135.83	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-05-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description