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- PDB-1t5a: Human Pyruvate Kinase M2 -

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Basic information

Entry
Database: PDB / ID: 1t5a
TitleHuman Pyruvate Kinase M2
ComponentsPyruvate kinase, M2 isozyme
KeywordsTRANSFERASE / alpha8-beta8 barrel / beta sheets / alpha helices
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / histone H3T11 kinase activity / programmed cell death / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding ...pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / histone H3T11 kinase activity / programmed cell death / 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 / 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 / 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 / cytosol / cytoplasm
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / 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 ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / 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 / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / : / OXALATE ION / PHOSPHATE ION / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDombrauckas, J.D. / Santarsiero, B.D. / Mesecar, A.D.
CitationJournal: Biochemistry / Year: 2005
Title: Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis.
Authors: Dombrauckas, J.D. / Santarsiero, B.D. / Mesecar, A.D.
History
DepositionMay 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 21, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase, M2 isozyme
B: Pyruvate kinase, M2 isozyme
C: Pyruvate kinase, M2 isozyme
D: Pyruvate kinase, M2 isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,70144
Polymers248,5134
Non-polymers4,18840
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27060 Å2
ΔGint-172 kcal/mol
Surface area71490 Å2
MethodPISA
2
A: Pyruvate kinase, M2 isozyme
C: Pyruvate kinase, M2 isozyme
hetero molecules

B: Pyruvate kinase, M2 isozyme
D: Pyruvate kinase, M2 isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,70144
Polymers248,5134
Non-polymers4,18840
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area22990 Å2
ΔGint-147 kcal/mol
Surface area75560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.209, 145.006, 159.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe functional tetramer is present in the assymmetric unit

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Pyruvate kinase, M2 isozyme


Mass: 62128.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM2, PKM / Plasmid: pJDAM-His / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3)pLysS / References: UniProt: P14618, pyruvate kinase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 171 molecules

#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.4 M Diammonium phosphate, glycerol, PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.91995 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91995 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 62359 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.7 / Redundancy: 11.5 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.7 / % possible all: 93

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A49

1a49


Resolution: 2.8→20 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: NCS GROUP NO. 1: EFFECTIVE FORCE CONSTANT FOR NCS POSITIONAL RESTRAINTS = 200.00 KCAL/MOL-A**2. TARGET DEVIATION OF NCS RELATED B FACTORS FROM AVERAGE = 2.000 A**2. NOTE: THE FIRST ...Details: NCS GROUP NO. 1: EFFECTIVE FORCE CONSTANT FOR NCS POSITIONAL RESTRAINTS = 200.00 KCAL/MOL-A**2. TARGET DEVIATION OF NCS RELATED B FACTORS FROM AVERAGE = 2.000 A**2. NOTE: THE FIRST EQUIVALENCE SET DEFINED IN A GROUP IS TAKEN AS THE REFERENCE. NCS GROUP 1 HAS 4 SETS OF EQUIVALENT ATOMS: EQUIVALENCE SET 2 : R.M.S. DIFF. BETWEEN MOLECULE AND REFERENCE FOR SELECTED ATOMS = 0.0824. EQUIVALENCE SET 3 : R.M.S. DIFF. BETWEEN MOLECULE AND REFERENCE FOR SELECTED ATOMS = 0.0929. EQUIVALENCE SET 4 : R.M.S. DIFF. BETWEEN MOLECULE AND REFERENCE FOR SELECTED ATOMS = 0.1281.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2850 4.7 %random
Rwork0.231 ---
all-59968 --
obs-57057 96.4 %-
Displacement parametersBiso mean: 69.4 Å2
Baniso -1Baniso -2Baniso -3
1--12.02 Å20 Å20 Å2
2--10.53 Å20 Å2
3---1.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15884 0 252 135 16271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.42 474 -
Rwork0.39 --
obs-9036 93.2 %

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