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- PDB-2vk8: Crystal structure of the Saccharomyces cerevisiae pyruvate decarb... -

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Basic information

Entry
Database: PDB / ID: 2vk8
TitleCrystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with its substrate
ComponentsPYRUVATE DECARBOXYLASE ISOZYME 1
KeywordsLYASE / ASYMMETRIC ACTIVE SITES / PHENYLALANINE CATABOLISM / TRYPTOPHAN CATABOLISM / THIAMINE PYROPHOSPHATE / DIMER OF DIMERS / PHOSPHORYLATION / ALLOSTERIC ENZYME / TDP / TPP / NUCLEUS / PYRUVATE / CYTOPLASM / BRANCHED-CHAIN AMINO ACID CATABOLISM / SUBSTRATE ACTIVATION / THIAMINE DIPHOSPHATE / MAGNESIUM / ACETYLATION / METAL-BINDING / DECARBOXYLASE
Function / homology
Function and homology information


phenylpyruvate decarboxylase / branched-chain-2-oxoacid decarboxylase / phenylpyruvate decarboxylase activity / branched-chain-2-oxoacid decarboxylase activity / indolepyruvate decarboxylase / pyruvate fermentation to ethanol / indolepyruvate decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases ...phenylpyruvate decarboxylase / branched-chain-2-oxoacid decarboxylase / phenylpyruvate decarboxylase activity / branched-chain-2-oxoacid decarboxylase activity / indolepyruvate decarboxylase / pyruvate fermentation to ethanol / indolepyruvate decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / branched-chain amino acid catabolic process / L-tryptophan catabolic process / L-phenylalanine catabolic process / thiamine pyrophosphate binding / magnesium ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Thiamine pyrophosphate (TPP)-dependent enzyme / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding ...: / Thiamine pyrophosphate (TPP)-dependent enzyme / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-HYDROXYPROPANOIC ACID / THIAMINE DIPHOSPHATE / Pyruvate decarboxylase isozyme 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsKutter, S. / Weik, M. / Weiss, M.S. / Konig, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.
Authors: Kutter, S. / Weiss, M.S. / Wille, G. / Golbik, R. / Spinka, M. / Konig, S.
History
DepositionDec 17, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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: PYRUVATE DECARBOXYLASE ISOZYME 1
B: PYRUVATE DECARBOXYLASE ISOZYME 1
C: PYRUVATE DECARBOXYLASE ISOZYME 1
D: PYRUVATE DECARBOXYLASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,50316
Polymers246,3444
Non-polymers2,15912
Water32,7511818
1
A: PYRUVATE DECARBOXYLASE ISOZYME 1
B: PYRUVATE DECARBOXYLASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2518
Polymers123,1722
Non-polymers1,0796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-59.2 kcal/mol
Surface area45250 Å2
MethodPQS
2
C: PYRUVATE DECARBOXYLASE ISOZYME 1
D: PYRUVATE DECARBOXYLASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2518
Polymers123,1722
Non-polymers1,0796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-66 kcal/mol
Surface area45010 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.980, 190.510, 84.140
Angle α, β, γ (deg.)90.00, 113.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PYRUVATE DECARBOXYLASE ISOZYME 1 / PYRUVATE DECARBOXYLASE


Mass: 61586.043 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PUC 18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P06169, pyruvate decarboxylase
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1818 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 477 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 477 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 477 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 477 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLU 477 TO GLN ENGINEERED RESIDUE IN CHAIN D, GLU 477 TO GLN

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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: 2.37 Å3/Da / Density % sol: 48.1 % / Description: NONE
Crystal growTemperature: 273.15 K / Method: vapor diffusion, hanging drop / pH: 6.35
Details: 15MM CITRATE, 1.67MM MES, 315MM PYRUVATE, 1MM NADH, 0.001MG/ML ALCOHOL DEHYDROGENASE, 1.67MM TDP, 1.67MM MAGNESIUM SULFATE, 1.67MM DTT, 11.25% PEG2000, 11.25% PEG 6000, 1.1MG SCPDC/ML, PH 6. ...Details: 15MM CITRATE, 1.67MM MES, 315MM PYRUVATE, 1MM NADH, 0.001MG/ML ALCOHOL DEHYDROGENASE, 1.67MM TDP, 1.67MM MAGNESIUM SULFATE, 1.67MM DTT, 11.25% PEG2000, 11.25% PEG 6000, 1.1MG SCPDC/ML, PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.42→99 Å / Num. obs: 427276 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.5
Reflection shellResolution: 1.42→1.44 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREP- AUTO MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VK1

2vk1


Resolution: 1.42→95.35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1068 0.3 %RANDOM
Rwork0.181 ---
obs0.181 425935 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.19 Å2
2---0.06 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.42→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17292 0 132 1818 19242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02217787
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.96624192
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3952244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99825.189740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.571152964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6121560
X-RAY DIFFRACTIONr_chiral_restr0.530.22780
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213316
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.29046
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.212501
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.21542
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5571.511172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.027218044
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6736615
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5924.56148
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 85 -
Rwork0.254 31527 -
obs--99.77 %

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