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- PDB-1tkc: SPECIFICITY OF COENZYME BINDING IN THIAMIN DIPHOSPHATE DEPENDENT ... -

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Basic information

Entry
Database: PDB / ID: 1tkc
TitleSPECIFICITY OF COENZYME BINDING IN THIAMIN DIPHOSPHATE DEPENDENT ENZYMES: CRYSTAL STRUCTURES OF YEAST TRANSKETOLASE IN COMPLEX WITH ANALOGS OF THIAMIN DIPHOSPHATE
ComponentsTRANSKETOLASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. ...Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6'-METHYL-THIAMIN DIPHOSPHATE / Transketolase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsSchneider, G. / Koenig, S.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Specificity of coenzyme binding in thiamin diphosphate-dependent enzymes. Crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate.
Authors: Konig, S. / Schellenberger, A. / Neef, H. / Schneider, G.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Refined Structure of Transketolase from Saccharomyces Cerevisae at 2.0 Angstrom Resolution
Authors: Nikkola, M. / Lindqvist, Y. / Schneider, G.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Yeast Tkl1 Gene Encodes a Transketolase that is Required for Efficient Glycolysis and Biosynthesis of Aromatic Amino Acids
Authors: Sundstrom, M. / Lindqvist, Y. / Schneider, G. / Hellman, U. / Ronne, H.
#3: Journal: Embo J. / Year: 1992
Title: Three-Dimensional Structure of Transketolase, a Thiamine Diphosphate Dependent Enzyme, at 2.5 Angstroms Resolution
Authors: Lindqvist, Y. / Schneider, G. / Ermler, U. / Sundstrom, M.
#4: Journal: J.Biol.Chem. / Year: 1989
Title: Preliminary Crystallographic Data for Transketolase from Yeast
Authors: Schneider, G. / Sundstrom, M. / Lindqvist, Y.
History
DepositionFeb 7, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSKETOLASE
B: TRANSKETOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,2676
Polymers147,3102
Non-polymers9574
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-75 kcal/mol
Surface area41550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.300, 113.300, 160.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.784, 0.001, -0.621), (-1, -0.002), (-0.621, -0.001, 0.784)
Vector: 25.044, 132.157, 8.813)
DetailsTHE TRANSFORMATION PRESENTED ON MTRIX RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein TRANSKETOLASE


Mass: 73655.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23254, transketolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-M6T / 6'-METHYL-THIAMIN DIPHOSPHATE


Mass: 438.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N4O7P2S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
27.5 %PEG60001drop
325 mMglycylglycine1drop
42 mMthiamine-PP1drop
550 mMglycylglycine1reservoir
62 mMthiamine-PP1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 24737 / % possible obs: 72.5 % / Num. measured all: 56543 / Rmerge(I) obs: 0.053

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.7→15 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.152 -
obs0.152 24737
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10396 0 56 0 10452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.152 / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.3
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_deg1.4

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