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- PDB-6gua: Xylulose 5-phosphate phosphoketolase from Lactococcus lactis -

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Basic information

Entry
Database: PDB / ID: 6gua
TitleXylulose 5-phosphate phosphoketolase from Lactococcus lactis
ComponentsProbable phosphoketolase
KeywordsLYASE / THIAMINE DIPHOSPHATE-DEPENDENT ENZYME / ALPHA-BETA FOLD / HOMODIMER
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Aldehyde-lyases / aldehyde-lyase activity / carbohydrate metabolic process
Similarity search - Function
Probable phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. ...Probable phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. / Phosphoketolase signature 2. / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
PHOSPHATE ION / THIAMINE DIPHOSPHATE / Probable phosphoketolase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SOLUTION SCATTERING / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsScheidig, A.J. / Szedlacsek, S.E.
Citation
Journal: J Struct Biol / Year: 2019
Title: Crystal structure of a xylulose 5-phosphate phosphoketolase. Insights into the substrate specificity for xylulose 5-phosphate.
Authors: A J Scheidig / D Horvath / S E Szedlacsek /
Abstract: Phosphoketolases (PK) are TPP-dependent enzymes which play essential roles in carbohydrate metabolism of numerous bacteria. Depending on the substrate specificity PKs can be subdivided into xylulose ...Phosphoketolases (PK) are TPP-dependent enzymes which play essential roles in carbohydrate metabolism of numerous bacteria. Depending on the substrate specificity PKs can be subdivided into xylulose 5-phosphate (X5P) specific PKs (XPKs) and PKs which accept both X5P and fructose 6-phosphate (F6P) (XFPKs). Despite their key metabolic importance, so far only the crystal structures of two XFPKs have been reported. There are no reported structures for any XPKs and for any complexes between PK and substrate. One of the major unknowns concerning PKs mechanism of action is related to the structural determinants of PKs substrate specificity for X5P or F6P. We report here the crystal structure of XPK from Lactococcus lactis (XPK-Ll) at 2.1 Å resolution. Using small angle X-ray scattering (SAXS) we proved that XPK-Ll is a dimer in solution. Towards better understanding of PKs substrate specificity, we performed flexible docking of TPP-X5P and TPP-F6P on crystal structures of XPK-Ll, two XFPKs and transketolase (TK). Calculated structure-based binding energies consistently support XPK-Ll preference for X5P. Analysis of structural models thus obtained show that substrates adopt moderately different conformation in PKs active sites following distinct networks of polar interactions. Based on the here reported structure of XPK-Ll we propose the most probable amino acid residues involved in the catalytic steps of reaction mechanism. Altogether our results suggest that PKs substrate preference for X5P or F6P is the outcome of a fine balance between specific binding network and dissimilar catalytic residues depending on the enzyme (XPK or XFPK) - substrate (X5P or F6P) couples.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2010
Title: Preliminary X-ray crystallographic analysis of the D-xylulose 5-phosphate phosphoketolase from Lactococcus lactis.
Authors: Petrareanu, G. / Balasu, M.C. / Zander, U. / Scheidig, A.J. / Szedlacsek, S.E.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable phosphoketolase
B: Probable phosphoketolase
C: Probable phosphoketolase
D: Probable phosphoketolase
E: Probable phosphoketolase
F: Probable phosphoketolase
G: Probable phosphoketolase
H: Probable phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)752,15732
Polymers747,8008
Non-polymers4,35724
Water108,0545998
1
A: Probable phosphoketolase
B: Probable phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,0398
Polymers186,9502
Non-polymers1,0896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13350 Å2
ΔGint-93 kcal/mol
Surface area46620 Å2
MethodPISA
2
C: Probable phosphoketolase
D: Probable phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,0398
Polymers186,9502
Non-polymers1,0896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-95 kcal/mol
Surface area47140 Å2
MethodPISA
3
E: Probable phosphoketolase
F: Probable phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,0398
Polymers186,9502
Non-polymers1,0896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-93 kcal/mol
Surface area47260 Å2
MethodPISA
4
G: Probable phosphoketolase
H: Probable phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,0398
Polymers186,9502
Non-polymers1,0896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13340 Å2
ΔGint-92 kcal/mol
Surface area46600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.100, 141.500, 161.150
Angle α, β, γ (deg.)90.000, 90.290, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Probable phosphoketolase


Mass: 93474.992 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
Gene: LL1502, L138230 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CFH4, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5998 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
SOLUTION SCATTERING

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 17 % (w/v) PEG-3350, 0.2 M sodium isothiocyanate,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.931 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 21, 2005
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.95→44.3 Å / Num. obs: 501022 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.079 / Rrim(I) all: 0.152 / Net I/σ(I): 6.79
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 44418 / CC1/2: 0.183 / Rpim(I) all: 0.548 / Rrim(I) all: 0.913 / % possible all: 86.6

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TRK

1trk


Resolution: 1.95→44.3 Å / Data cutoff high absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 25031 5 %Random selection
Rwork0.212 ---
obs-500681 97.3 %-
Displacement parametersBiso mean: 28.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52634 0 256 5998 58888
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection% reflection
Rfree0.427 2221 5 %
Rwork0.402 44415 -
obs--86.6 %

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