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

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Basic information

Entry
Database: PDB / ID: 1uxv
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+)
KeywordsOXIDOREDUCTASE / GAPN / ALDH / AMP / GLYCERALDEHYDE 3-PHOSPHATE / GLYCOLYSIS / REGULATION / CATALYSIS
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) activity / 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, C-terminal / Aldehyde dehydrogenase, N-terminal ...: / : / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesTHERMOPROTEUS TENAX (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.4Dec 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,2984
Polymers54,1841
Non-polymers1,1143
Water5,170287
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)221,19216
Polymers216,7374
Non-polymers4,45412
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)185.208, 185.208, 134.134
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+)


Mass: 54184.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AMP AND NADP(H) 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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*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


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
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, 50 MM AMP

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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: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 52301 / % possible obs: 92 % / Redundancy: 10 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 33
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / % possible all: 66

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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: 2.35→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
Rfree0.243 1278 2.5 %RANDOM
Rwork0.226 ---
obs0.226 50174 92 %-
Displacement parametersBiso mean: 62 Å2
Baniso -1Baniso -2Baniso -3
1-4.941 Å2-1.823 Å20 Å2
2--4.941 Å20 Å2
3----9.881 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 72 287 4133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
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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