6TER | pdb_00006ter

Crystal structure of a galactokinase from Bifidobacterium infantis in complex with Galactose

• PDB DOI: https://doi.org/10.2210/pdb6TER/pdb

• Classification: TRANSFERASE
• Organism(s): Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-12 Released: 2020-06-10 
• Deposition Author(s): Keenan, T., Parmeggiani, F., Fontenelle, C.Q., Malassis, J., Vendeville, J., Offen, W.A., Both, P., Huang, K., Marchesi, A., Heyam, A., Young, C., Charnock, S., Davies, G.J., Linclau, B., Flitsch, S.L., Fascione, M.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.308 (Depositor), 0.312 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

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

• PubMed: 32619452 
• 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.

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Organizational Affiliation: 
• Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
Prozomix Limited, Haltwhistle Industrial Estate, Haltwhistle, Northumberland NE49 9HA, UK.
Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. Electronic address: [e-mail].
Department of Chemistry, University of York, Heslington, York YO10 5DD, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 190.94 kDa 
• Atom Count: 14,073 
• Modeled Residue Count: 1,668 
• Deposited Residue Count: 1,716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactokinase	A, B, C, D	429	Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088	Mutation(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

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	BA [auth A], Z [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GAL (Subject of Investigation/LOI)	FA [auth A], ZA [auth B]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
GLA (Subject of Investigation/LOI)	EA [auth A], NB [auth C], YA [auth B], YB [auth D]	alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N
PGE	UA [auth B], W [auth A], X [auth A], Y [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS	RB [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	DA [auth A], G [auth A], H [auth A], IA [auth B], J [auth A], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], MB [auth C], N [auth A], OA [auth B], P [auth A], R [auth A], RA [auth B], S [auth A], SB [auth D], TA [auth B], U [auth A], V [auth A], VA [auth B], VB [auth D], WA [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	AA [auth A], CA [auth A], DB [auth C], E [auth A], EB [auth C], F [auth A], FB [auth C], GB [auth C], HA [auth B], HB [auth C], I [auth A], IB [auth C], LB [auth C], M [auth A], MA [auth B], NA [auth B], O [auth A], PA [auth B], Q [auth A], QA [auth B], SA [auth B], T [auth A], TB [auth D], UB [auth D], WB [auth D], XA [auth B], XB [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	GA [auth A], PB [auth C], QB [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	AB [auth B], AC [auth D], BB [auth B], CB [auth B], OB [auth C], ZB [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.308 (Depositor), 0.312 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.32	α = 90
b = 164.929	β = 94.97
c = 113.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Keenan, T., Parmeggiani, F., Fontenelle, C.Q., Malassis, J., Vendeville, J., Offen, W.A., Both, P., Huang, K., Marchesi, A., Heyam, A., Young, C., Charnock, S., Davies, G.J., Linclau, B., Flitsch, S.L., Fascione, M.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M02847X/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M028836/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M028941/1

Revision History  

• 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