7EHR | pdb_00007ehr

Levansucrase from Brenneria sp. EniD 312 at 1.33 angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 
    0.176 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.145 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7EHR

This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Levansucrase from the Gram-Negative Bacterium Brenneria Provides Insights into Its Product Size Specificity.

Xu, W.Ni, D.Hou, X.Pijning, T.Guskov, A.Rao, Y.Mu, W.

(2022) J Agric Food Chem 70: 5095-5105

  • DOI: https://doi.org/10.1021/acs.jafc.2c01225
  • Primary Citation Related Structures: 
    7EHR, 7EHS, 7EHT, 7FDZ

  • PubMed Abstract: 

    Microbial levansucrases (LSs, EC 2.4.1.10) have been widely studied for the synthesis of β-(2,6)-fructans (levan) from sucrose. LSs synthesize levan-type fructo-oligosaccharides, high-molecular-mass levan polymer or combinations of both. Here, we report crystal structures of LS from the G - -bacterium Brenneria sp. EniD 312 ( Brs -LS) in its apo form, as well as of two mutants (A154S, H327A) targeting positions known to affect LS reaction specificity. In addition, we report a structure of Brs -LS complexed with sucrose, the first crystal structure of a G - -LS with a bound substrate. The overall structure of Brs -LS is similar to that of G - - and G + -LSs, with the nucleophile (D68), transition stabilizer (D225), and a general acid/base (E309) in its active site. The H327A mutant lacks an essential interaction with glucosyl moieties of bound substrates in subsite +1, explaining the observed smaller products synthesized by this mutant. The A154S mutation affects the hydrogen-bond network around the transition stabilizing residue (D225) and the nucleophile (D68), and may affect the affinity of the enzyme for sucrose such that it becomes less effective in transfructosylation. Taken together, this study provides novel insights into the roles of structural elements and residues in the product specificity of LSs.


  • Organizational Affiliation
    • State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.

Macromolecule Content 

  • Total Structure Weight: 51.64 kDa 
  • Atom Count: 4,034 
  • Modeled Residue Count: 417 
  • Deposited Residue Count: 443 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Levansucrase443Brenneria sp. EniD312Mutation(s): 0 
Gene Names: BrE312_3941
EC: 2.4.1.10
UniProt
Find proteins for A0ACD6B9Q1 (Brenneria sp. EniD312)
Explore A0ACD6B9Q1 
Go to UniProtKB:  A0ACD6B9Q1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9Q1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4

Query on PE4



Download:Ideal Coordinates CCD File
I [auth A]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
H [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free:  0.176 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.145 (DCC) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98α = 90
b = 98β = 90
c = 213.539γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31922073

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2022-05-11
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description