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- PDB-1uxt: Structural basis for allosteric regulation and substrate specific... -

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Basic information

Entry
Database: PDB / ID: 1uxt
TitleStructural basis for allosteric regulation and substrate specificity of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) from Thermoproteus tenax
ComponentsGLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+)Glyceraldehyde-3-phosphate dehydrogenase (NADP+)
KeywordsOXIDOREDUCTASE / GAPN / ALDH / GLUCOSE 1-PHOSPHATE / NAD / GLYCOLYSIS / REGULATION / CATATYSIS
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / metabolic process / NAD binding / NADP binding
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-O-phosphono-alpha-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesTHERMOPROTEUS TENAX (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLorentzen, E. / Hensel, R. / Pohl, E.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural Basis of Allosteric Regulation and Substrate Specificity of the Non-Phosphorylating Glyceraldehyde 3-Phosphate Dehydrogenase from Thermoproteus Tenax
Authors: Lorentzen, E. / Hensel, R. / Knura, T. / Ahmed, H. / Pohl, E.
History
DepositionMar 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr1_symmetry / _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.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1654
Polymers54,2181
Non-polymers9473
Water4,828268
1
A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+)
hetero molecules

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+)
hetero molecules

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+)
hetero molecules

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,66016
Polymers216,8734
Non-polymers3,78612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation12_565x,x-y+1,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)185.347, 185.347, 134.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+) / Glyceraldehyde-3-phosphate dehydrogenase (NADP+)


Mass: 54218.367 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GLUCOSE 1-PHOSPHATE AND NAD BOUND NONCOVALENTLY / Source: (gene. exp.) THERMOPROTEUS TENAX (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O57693, glyceraldehyde-3-phosphate dehydrogenase (NADP+)
#2: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION LEU 378 PHE IN CHAIN A
Sequence detailsSER 402 LEU IS DUE TO A SEQUENCING ERROR. THE AUTHORS INDICATE THAT THE SERINE REPORTED IN SWISS- ...SER 402 LEU IS DUE TO A SEQUENCING ERROR. THE AUTHORS INDICATE THAT THE SERINE REPORTED IN SWISS-PROT IS DUE TO A SEQUENCING ERROR.

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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: 6 Å3/Da / Density % sol: 80 %
Crystal growpH: 5.6
Details: 2M SODIUM FORMATE PH 5.6, 0.1 M SODIUM ACETATE PH 5.6,1 MM GLUCOSE 1-PHOSPHATE, 10 MM NAD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8453
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 67596 / % possible obs: 98 % / Redundancy: 13 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 23
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 13 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 7 / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KY8

1ky8


Resolution: 2.2→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 1-2 NOT MODELED, RESIDUES 499-501 AS ALANINES
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1673 2.5 %RANDOM
Rwork0.224 ---
obs0.224 64609 98 %-
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1-6.304 Å25.762 Å20 Å2
2---4.99 Å20 Å2
3----1.314 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 61 268 4106
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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