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- PDB-6zmj: Crystal structure of human GFAT-1 R203H -

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Basic information

Entry
Database: PDB / ID: 6zmj
TitleCrystal structure of human GFAT-1 R203H
ComponentsGlutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
KeywordsTRANSFERASE / Glutamine fructose-6-phosphate amidotransferase / GFAT / Ntn hydrolase
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 / carbohydrate derivative binding / energy reserve metabolic process / protein N-linked glycosylation ...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 / carbohydrate derivative binding / energy reserve metabolic process / protein N-linked glycosylation / fructose 6-phosphate 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 / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
GLUCOSE-6-PHOSPHATE / GLUTAMIC ACID / Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.774 Å
AuthorsRuegenberg, S. / Mayr, F. / Miethe, S. / Atanassov, I. / Baumann, U. / Denzel, M.S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research01GQ1423A Germany
European CommissionERC-2014-StG-640254-MetAGEn Germany
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
Citation
Journal: Nat Commun / Year: 2021
Title: Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1.
Authors: Ruegenberg, S. / Mayr, F.A.M.C. / Atanassov, I. / Baumann, U. / Denzel, M.S.
#1: Journal: Biorxiv / Year: 2020
Title: Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1
Authors: Ruegenberg, S. / Mayr, F. / Miethe, S. / Atanassov, I. / Baumann, U. / Denzel, M.S.
History
DepositionJul 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
B: Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,0215
Polymers155,3542
Non-polymers6673
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer, light scattering, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-22 kcal/mol
Surface area48690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.766, 152.766, 164.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 77676.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFPT1, GFAT, GFPT / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q06210, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Chemical ChemComp-G6Q / GLUCOSE-6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis tris propane pH 8.75, 0.2 M Potassium sodium tartrae, 20 % PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.774→48.653 Å / Num. obs: 49792 / % possible obs: 99.75 % / Redundancy: 13.3 % / CC1/2: 0.997 / Net I/σ(I): 14.05
Reflection shellResolution: 2.774→2.873 Å / Num. unique obs: 4773 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIXdev_2499refinement
PDB_EXTRACT3.25data extraction
XDSMar 15, 2019data reduction
XDSMar 15, 2019data scaling
PHENIXdev_2499phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R4E

6r4e


Resolution: 2.774→48.653 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 1993 4 %
Rwork0.2005 47794 -
obs0.2021 49787 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 419.52 Å2 / Biso mean: 104.9774 Å2 / Biso min: 29.96 Å2
Refinement stepCycle: final / Resolution: 2.774→48.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10267 0 76 20 10363
Biso mean--64.68 42.46 -
Num. residues----1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210485
X-RAY DIFFRACTIONf_angle_d0.4514153
X-RAY DIFFRACTIONf_chiral_restr0.0421619
X-RAY DIFFRACTIONf_plane_restr0.0021817
X-RAY DIFFRACTIONf_dihedral_angle_d12.586366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.774-2.84340.3641460.3292325297
2.8434-2.92030.32681200.3043371100
2.9203-3.00620.33241560.28033355100
3.0062-3.10320.31841530.2673366100
3.1032-3.21410.32651230.26543395100
3.2141-3.34270.31611440.24463377100
3.3427-3.49480.23981380.21783386100
3.4948-3.6790.24441390.19253402100
3.679-3.90940.20631490.17913403100
3.9094-4.21110.23111400.16473403100
4.2111-4.63460.20711380.15623452100
4.6346-5.30450.18631480.15293454100
5.3045-6.68040.24311470.20553501100
6.6804-48.6530.20691520.19463677100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3887-0.2986-0.02872.93290.04322.50710.09920.1992-0.1352-0.2572-0.1074-0.62450.22060.627-0.00860.39430.09930.09830.58560.08270.49885.440753.3538-74.1897
21.98250.710.27562.44590.13851.0087-0.02470.10530.29520.15340.04280.2555-0.1030.0104-0.00630.38270.0254-0.02510.34530.03570.3672-12.834751.3683-38.197
30.4215-0.39550.04340.6003-0.58351.2676-0.0047-0.9246-0.26210.946-0.07330.3216-0.0969-0.40860.05361.8837-0.15770.03511.90220.061.4065-12.542834.73779.8155
42.48740.50130.35391.84310.22791.2770.1452-0.0985-0.36680.4567-0.034-0.25660.13260.2074-0.10040.48180.0215-0.12740.34140.03590.42722.90329.7486-25.991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 314 )A2 - 314
2X-RAY DIFFRACTION2chain 'A' and (resid 315 through 672 )A315 - 672
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 314 )B2 - 314
4X-RAY DIFFRACTION4chain 'B' and (resid 315 through 680 )B315 - 680

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