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- PDB-2zj3: Isomerase domain of human glucose:fructose-6-phosphate amidotrans... -

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Basic information

Entry
Database: PDB / ID: 2zj3
TitleIsomerase domain of human glucose:fructose-6-phosphate amidotransferase
ComponentsGlucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1
KeywordsTRANSFERASE / glucosamine-6-phosphate synthase / aldose/ketose isomerase / Rossmann-like fold / Alternative splicing / Aminotransferase / Glutamine amidotransferase / Phosphoprotein
Function / homology
Function and homology information


Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process ...Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / circadian regulation of gene expression / extracellular exosome / cytosol
Similarity search - Function
Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / Glutamine amidotransferase type 2 domain profile. / SIS domain / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Nucleophile aminohydrolases, N-terminal / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakaishi, Y. / Bando, M. / Kondo, K. / Tsuge, H.
CitationJournal: Febs Lett. / Year: 2009
Title: Structural analysis of human glutamine:fructose-6-phosphate amidotransferase, a key regulator in type 2 diabetes
Authors: Nakaishi, Y. / Bando, M. / Shimizu, H. / Watanabe, K. / Goto, F. / Tsuge, H. / Kondo, K. / Komatsu, M.
History
DepositionFeb 29, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 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: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5792
Polymers42,3191
Non-polymers2601
Water4,990277
1
A: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1
hetero molecules

A: Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1594
Polymers84,6382
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area6230 Å2
ΔGint-11 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.652, 78.652, 274.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-890-

HOH

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Components

#1: Protein Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 / Glutamine:fructose 6 phosphate amidotransferase 1 / Hexosephosphate aminotransferase 1 / D-fructose- ...Glutamine:fructose 6 phosphate amidotransferase 1 / Hexosephosphate aminotransferase 1 / D-fructose-6-phosphate amidotransferase 1 / GFAT 1 / GFAT1


Mass: 42319.133 Da / Num. of mol.: 1
Fragment: SIS(Sugar ISomerase) domains, UNP Residues 332-699
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+RIL
References: UniProt: Q06210, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% Isoporpanol, 0.04M Tris, 0.08M Ammonium acetate, 12% glycerol 10-fold excess of Fructose-6-Phosphate, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Aug 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→29.88 Å / Num. obs: 34205 / % possible obs: 98.9 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOQ

1moq


Resolution: 1.9→29.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.696 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1720 5 %RANDOM
Rwork0.185 ---
obs0.187 32485 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 16 277 3159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222924
X-RAY DIFFRACTIONr_bond_other_d0.0010.022003
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9843943
X-RAY DIFFRACTIONr_angle_other_deg1.84834911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71123.92125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79215557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3651522
X-RAY DIFFRACTIONr_chiral_restr0.1330.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined0.2250.2655
X-RAY DIFFRACTIONr_nbd_other0.1970.22152
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21464
X-RAY DIFFRACTIONr_nbtor_other0.0890.21553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3621.52347
X-RAY DIFFRACTIONr_mcbond_other0.2421.5742
X-RAY DIFFRACTIONr_mcangle_it1.49222939
X-RAY DIFFRACTIONr_scbond_it2.75231233
X-RAY DIFFRACTIONr_scangle_it3.9474.51004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 123 -
Rwork0.187 2335 -
obs--97.69 %

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