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- PDB-1e7m: ACTIVE SITE MUTANT (D177->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE... -

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Basic information

Entry
Database: PDB / ID: 1e7m
TitleACTIVE SITE MUTANT (D177->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES
ComponentsGLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (CHOH(D) - NAD(P)) / GLUCOSE METABOLISM
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase [NAD(P)+] / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / NADP binding / cytosol
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLEUCONOSTOC MESENTEROIDES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsAdams, M.J. / Cosgrove, M.S. / Gover, S.
Citation
Journal: Biochemistry / Year: 2000
Title: An Examination of the Role of Asp-177 in the His-Asp Catalytic Dyad of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase: X-Ray Structure and Ph Dependence of Kinetic Parameters of ...Title: An Examination of the Role of Asp-177 in the His-Asp Catalytic Dyad of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase: X-Ray Structure and Ph Dependence of Kinetic Parameters of the D177N Mutant Enzyme
Authors: Cosgrove, M.S. / Gover, S. / Naylor, C.E. / Vandeputte-Rutten, L. / Adams, M.J. / Levy, H.R.
#1: Journal: Structure / Year: 1994
Title: The Three-Dimensional Structure of Glucose 6-Phosphate Dehydrogenase from Leuconostoc Mesenteroides Refined at 2 Angstroms Resolution
Authors: Rowland, P. / Basak, A.K. / Gover, S. / Levy, H.R. / Adams, M.J.
#2: Journal: Biochemistry / Year: 1998
Title: On the Mechanism of the Reaction Catalysed by Glucose 6-Phosphate Dehydrogenase
Authors: Cosgrove, M.S. / Naylor, C. / Paludin, S. / Adams, M.J. / Levy, H.R.
History
DepositionAug 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.6May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.7May 1, 2024Group: 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 / 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.status_code_sf / _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
Remark 650 HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO 2.0A L. MESENTEROIDES ... HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO 2.0A L. MESENTEROIDES STRUCTURE, 1DPG. HELIX_ID: A,BEND AT K21 IS CONSEQUENCE OF CONSERVED P24. HELIX_ID: B,THE LAST TURN IS 3_10 (CLASS 5). HELIX_ID: D,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: F,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID:I', PART OF HELIX I IN 1DPG. RESIDUES 235-239 DISTORTED BY SIDECHAIN INTERACTION OF N239 WITH D235.
Remark 700 SHEET DETERMINATION METHOD: INITIAL AND TERMINAL RESIDUES ARE AS DEFINED BY PROCHECK. REGISTRATION ... SHEET DETERMINATION METHOD: INITIAL AND TERMINAL RESIDUES ARE AS DEFINED BY PROCHECK. REGISTRATION IS AS GIVEN BY HYDROGEN BONDS AND IN THE CASE OF SHEET COE INVOLVES RESIDUES THAT IMMEDIATELY PRECEDE EACH SHEET ELEMENT. THIS IS DONE TO PRESERVE OBSERVED CONSISTENCY WITH NATIVE STRUCTURE 1DPG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4092
Polymers54,3691
Non-polymers401
Water1,22568
1
A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules

A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8174
Polymers108,7372
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5480 Å2
ΔGint-50.1 kcal/mol
Surface area45780 Å2
MethodPQS
Unit cell
Length a, b, c (Å)130.300, 44.400, 92.800
Angle α, β, γ (deg.)90.00, 106.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE / G6PD


Mass: 54368.660 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEUCONOSTOC MESENTEROIDES (bacteria) / Description: SITE DIRECTED MUTAGENESIS / Gene: PLMZ/D177N / Plasmid: PUC-19/ASP177ASNPLMZ / Gene (production host): PLMZ/D177N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SU294
References: UniProt: P11411, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION ASP177ASN BETA-D-GLUCOSE 6-PHOSPHATE + NADP(+) = D-GLUCONO-DELTA- ...CHAIN A ENGINEERED MUTATION ASP177ASN BETA-D-GLUCOSE 6-PHOSPHATE + NADP(+) = D-GLUCONO-DELTA-LACTONE 6-PHOSPHATE + NADPH.

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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: 42.1 %
Description: MOLECULE LOCATED BY DIFFERENCE FOURIER AND RIGID-BODY REFINEMENT
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. IN THE WELL BUFFER: 20% W/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.5 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 15MG/ML, WITH 29MM NAD+.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlenzyme1drop
20.1 MTris-HCl1drop
329 mMNAD+1drop
420 %(v/v)PEG4001reservoir
50.1 MHEPES/NaOH1reservoir
60.2 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.54→30 Å / Num. obs: 15753 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.086 / Net I/σ(I): 12.7
Reflection shellResolution: 2.54→2.59 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.259 / % possible all: 85.6
Reflection
*PLUS
Num. measured all: 46259 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 85.6 % / Rmerge(I) obs: 0.259

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED COORDINATES OF APO-ENZYME IN THE SAME SPACEGROUP

Resolution: 2.54→24.2 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: BULK SOLVENT WAS MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.299 758 4.8 %RANDOM, USING XPLOR
Rwork0.222 ---
obs0.222 15750 95.1 %-
Displacement parametersBiso mean: 38.8 Å2
Refine analyzeLuzzati d res low obs: 24.2 Å / Luzzati sigma a obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.54→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 1 68 3909
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.94
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.41.5
X-RAY DIFFRACTIONx_mcangle_it4.972
X-RAY DIFFRACTIONx_scbond_it3.41.5
X-RAY DIFFRACTIONx_scangle_it4.972
LS refinement shellResolution: 2.54→2.63 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.479 49 5.4 %
Rwork0.387 853 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 14992
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.94

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