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- PDB-6gg5: Crystal structure of M2 PYK in complex with Tryptophan. -

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Basic information

Entry
Database: PDB / ID: 6gg5
TitleCrystal structure of M2 PYK in complex with Tryptophan.
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / Glycolysis / Pyruvate Kinase Activity
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding ...pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / Regulation of pyruvate metabolism / glycolytic process / non-specific protein-tyrosine kinase / cellular response to insulin stimulus / MHC class II protein complex binding / extracellular vesicle / : / protein tyrosine kinase activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cilium / cadherin binding / intracellular membrane-bounded organelle / 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
: / PHOSPHATE ION / TRYPTOPHAN / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMcNae, I.W. / Yuan, M. / Walkinshaw, M.D.
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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)242,55020
Polymers240,8174
Non-polymers1,73316
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17060 Å2
ΔGint-116 kcal/mol
Surface area66280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.880, 70.576, 168.502
Angle α, β, γ (deg.)90.00, 106.02, 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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#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.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 46.5 %
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: 3.2→72.54 Å / Num. obs: 36606 / % possible obs: 98.2 % / Redundancy: 2.9 % / Net I/σ(I): 7.5
Reflection shellResolution: 3.2→3.283 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: 3.2→72.54 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.847 / SU B: 68.313 / SU ML: 0.489 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26523 1769 4.9 %RANDOM
Rwork0.22836 ---
obs0.23016 34029 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.959 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å21.35 Å2
2---5.83 Å2-0 Å2
3---6 Å2
Refinement stepCycle: 1 / Resolution: 3.2→72.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14102 0 104 27 14233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01914468
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213981
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.97219558
X-RAY DIFFRACTIONr_angle_other_deg0.957332365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2151840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02523.465606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.608152585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.40115125
X-RAY DIFFRACTIONr_chiral_restr0.0740.22232
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022840
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_it1.2162.5997366
X-RAY DIFFRACTIONr_mcbond_other1.2162.5997365
X-RAY DIFFRACTIONr_mcangle_it2.2373.8959192
X-RAY DIFFRACTIONr_mcangle_other2.2373.8959193
X-RAY DIFFRACTIONr_scbond_it0.7082.6777102
X-RAY DIFFRACTIONr_scbond_other0.7082.6777102
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3974.00510363
X-RAY DIFFRACTIONr_long_range_B_refined3.73130.25315494
X-RAY DIFFRACTIONr_long_range_B_other3.73130.25315495
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)
11A315780.05
12B315780.05
21A256700.05
22C256700.05
31A257380.04
32D257380.04
41B259020.05
42C259020.05
51B259660.04
52D259660.04
61C259320.05
62D259320.05
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 149 -
Rwork0.342 2493 -
obs--98.62 %
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)
10.4082-0.13950.28590.1055-0.050.554-0.0020.06350.0433-0.0065-0.01660.00740.04710.11970.01850.45160.06830.0120.6768-0.0020.0169377.689-76.59205.753
20.2193-0.20190.05340.4498-0.14830.5335-0.0457-0.0185-0.0708-0.00560.0744-0.0712-0.0946-0.1425-0.02880.41430.06520.04820.6261-0.00320.1016318.749-36.116207.976
30.3733-0.3795-0.03940.42380.04310.6371-0.0756-0.0053-0.01110.01140.08850.01390.00130.002-0.01290.50070.00280.01190.5891-0.00140.0018337.028-48.349175.719
40.7388-0.2705-0.12160.5917-0.1820.4424-0.0047-0.084-0.0250.04460.00370.0307-0.01720.03370.0010.46420.0114-0.00580.61380.02010.0026347.748-80.673230.661
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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