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- PDB-6gg4: Crystal structure of M2 PYK in complex with Phenyalanine. -

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Basic information

Entry
Database: PDB / ID: 6gg4
TitleCrystal structure of M2 PYK in complex with Phenyalanine.
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / Glycolysis / Pyruvate Kinase Activity
Function / homology
Function and homology information


positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / protein tyrosine kinase activity / secretory granule lumen / collagen-containing extracellular matrix / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / phosphorylation / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily ...Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHENYLALANINE / PHOSPHATE ION / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsMcNae, I.W. / Yuan, M. / Walkinshaw, M.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Biochem. J. / Year: 2018
Title: An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor.
Authors: Yuan, M. / McNae, I.W. / Chen, Y. / Blackburn, E.A. / Wear, M.A. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Hupp, T. / Walkinshaw, M.D.
History
DepositionMay 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase PKM
B: Pyruvate kinase PKM
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,39420
Polymers240,8174
Non-polymers1,57716
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17110 Å2
ΔGint-114 kcal/mol
Surface area67310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.370, 70.340, 168.640
Angle α, β, γ (deg.)90.00, 106.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA23 - 53143 - 551
21PROPROBB23 - 53143 - 551
12VALVALAA23 - 53043 - 550
22VALVALCC23 - 53043 - 550
13VALVALAA23 - 53043 - 550
23VALVALDD23 - 53043 - 550
14VALVALBB23 - 53043 - 550
24VALVALCC23 - 53043 - 550
15VALVALBB23 - 53043 - 550
25VALVALDD23 - 53043 - 550
16PROPROCC23 - 53143 - 551
26PROPRODD23 - 53143 - 551

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Pyruvate kinase PKM / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate kinase 2/3 / Pyruvate kinase muscle isozyme / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / p58


Mass: 60204.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 10-16% PEG 3350, 100 mM sodium Cacodylate, 50 mM MgCl2, 100 mM KCl,
PH range: 7.2-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 2.46→162.1 Å / Num. obs: 80146 / % possible obs: 98.8 % / Redundancy: 5.8 % / Net I/σ(I): 14.2
Reflection shellResolution: 2.46→2.524 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fxj

4fxj


Resolution: 2.46→162.06 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / SU B: 16.742 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.461 / ESU R Free: 0.249 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22463 3904 4.9 %RANDOM
Rwork0.19665 ---
obs0.19808 75137 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.614 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å2-0 Å21 Å2
2---1.35 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.46→162.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14102 0 92 353 14547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01914470
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214001
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.97419556
X-RAY DIFFRACTIONr_angle_other_deg0.898332411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.30251844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89323.421608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.615152591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.76815127
X-RAY DIFFRACTIONr_chiral_restr0.0680.22234
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022846
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8925.2497370
X-RAY DIFFRACTIONr_mcbond_other1.8925.2497369
X-RAY DIFFRACTIONr_mcangle_it3.2147.8689198
X-RAY DIFFRACTIONr_mcangle_other3.2147.8689199
X-RAY DIFFRACTIONr_scbond_it1.9755.5497100
X-RAY DIFFRACTIONr_scbond_other1.9755.5497100
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3628.22310353
X-RAY DIFFRACTIONr_long_range_B_refined5.36161.74215363
X-RAY DIFFRACTIONr_long_range_B_other5.34761.69615328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A314780.05
12B314780.05
21A255840.06
22C255840.06
31A256760.05
32D256760.05
41B256340.05
42C256340.05
51B256900.05
52D256900.05
61C257120.05
62D257120.05
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 270 -
Rwork0.263 5603 -
obs--99.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4732-0.26480.23910.1653-0.18890.74260.01090.01260.0231-0.01260.00410.00280.02660.0779-0.01490.07310.0624-0.00850.1223-0.00870.033377.689-76.5902205.7526
20.3504-0.39690.05870.4754-0.11240.78390.02340.0173-0.0223-0.0189-0.0032-0.0135-0.0489-0.1431-0.02020.0460.0570.01610.10750.00830.081318.7491-36.1165207.976
30.2444-0.249-0.02450.3458-0.02460.6337-0.05640.01680.01480.0390.05190.01610.0144-0.00660.00450.12540.0218-0.01320.08110.01030.0274337.0282-48.3493175.7193
40.6838-0.2646-0.16240.4189-0.06560.6505-0.0265-0.1008-0.02010.03910.01130.0353-0.00670.03670.01530.09460.0311-0.00590.08130.01380.022347.7482-80.6729230.6611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 605
2X-RAY DIFFRACTION2B23 - 605
3X-RAY DIFFRACTION3C23 - 531
4X-RAY DIFFRACTION4D23 - 531

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