6TEQ | pdb_00006teq

Crystal structure of a galactokinase from Bifidobacterium infantis in complex with 2-deoxy-2-fluoro-galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.203 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Profiling Substrate Promiscuity of Wild-Type Sugar Kinases for Multi-fluorinated Monosaccharides.

Keenan, T.Parmeggiani, F.Malassis, J.Fontenelle, C.Q.Vendeville, J.B.Offen, W.Both, P.Huang, K.Marchesi, A.Heyam, A.Young, C.Charnock, S.J.Davies, G.J.Linclau, B.Flitsch, S.L.Fascione, M.A.

(2020) Cell Chem Biol 27: 1199

  • DOI: https://doi.org/10.1016/j.chembiol.2020.06.005
  • Primary Citation Related Structures: 
    6TEP, 6TEQ, 6TER

  • PubMed Abstract: 

    Fluorinated sugar-1-phosphates are of emerging importance as intermediates in the chemical and biocatalytic synthesis of modified oligosaccharides, as well as probes for chemical biology. Here we present a systematic study of the activity of a wide range of anomeric sugar kinases (galacto- and N-acetylhexosamine kinases) against a panel of fluorinated monosaccharides, leading to the first examples of polyfluorinated substrates accepted by this class of enzymes. We have discovered four new N-acetylhexosamine kinases with a different substrate scope, thus expanding the number of homologs available in this subclass of kinases. Lastly, we have solved the crystal structure of a galactokinase in complex with 2-deoxy-2-fluorogalactose, giving insight into changes in the active site that may account for the specificity of the enzyme toward certain substrate analogs.


  • Organizational Affiliation
    • Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.

Macromolecule Content 

  • Total Structure Weight: 188.88 kDa 
  • Atom Count: 15,169 
  • Modeled Residue Count: 1,673 
  • Deposited Residue Count: 1,716 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galactokinase
A, B, C, D
429Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088Mutation(s): 0 
Gene Names: Blon_2062
EC: 2.7.1.6
UniProt
Find proteins for B7GUI0 (Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12))
Explore B7GUI0 
Go to UniProtKB:  B7GUI0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7GUI0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES

Query on MES



Download:Ideal Coordinates CCD File
E [auth A],
J [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
GAF
(Subject of Investigation/LOI)

Query on GAF



Download:Ideal Coordinates CCD File
AB [auth D],
M [auth A],
PA [auth C],
Y [auth B]
2-deoxy-2-fluoro-alpha-D-galactopyranose
C6 H11 F O5
ZCXUVYAZINUVJD-DVKNGEFBSA-N
2FG
(Subject of Investigation/LOI)

Query on 2FG



Download:Ideal Coordinates CCD File
N [auth A],
QA [auth C],
X [auth B],
ZA [auth D]
2-deoxy-2-fluoro-beta-D-galactopyranose
C6 H11 F O5
ZCXUVYAZINUVJD-VFUOTHLCSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
JA [auth C],
LA [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
BA [auth C]
CA [auth C]
DA [auth C]
F [auth A]
FA [auth C]
BA [auth C],
CA [auth C],
DA [auth C],
F [auth A],
FA [auth C],
GA [auth C],
H [auth A],
K [auth A],
NA [auth C],
OA [auth C],
P [auth B],
RA [auth C],
S [auth B],
SA [auth C],
U [auth B],
VA [auth D],
W [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
BB [auth D]
EA [auth C]
G [auth A]
I [auth A]
IA [auth C]
BB [auth D],
EA [auth C],
G [auth A],
I [auth A],
IA [auth C],
KA [auth C],
L [auth A],
MA [auth C],
Q [auth B],
R [auth B],
T [auth B],
WA [auth D],
XA [auth D],
YA [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
HA [auth C],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth B]
CB [auth D]
DB [auth D]
O [auth A]
TA [auth C]
AA [auth B],
CB [auth D],
DB [auth D],
O [auth A],
TA [auth C],
UA [auth C],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.203 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.218α = 90
b = 164.386β = 95.94
c = 115.874γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M02847X/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M028836/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2020-09-30
    Changes: Database references, Structure summary
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Refinement description