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- PDB-6r4f: Crystal structure of human GFAT-1 in complex with Glucose-6-Phosphate -

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Basic information

Entry
Database: PDB / ID: 6r4f
TitleCrystal structure of human GFAT-1 in complex with Glucose-6-Phosphate
ComponentsGlutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
KeywordsTRANSFERASE / Glutamine fructose-6-phosphate aminotransferase / 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 / energy reserve metabolic process / carbohydrate derivative binding / 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 / energy reserve metabolic process / carbohydrate derivative binding / 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/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. ...Glucosamine-fructose-6-phosphate aminotransferase, isomerising / : / Glutamine amidotransferase domain / GlmS/AgaS, SIS domain 1 / GlmS/FrlB, SIS domain 2 / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
GLUCOSE-6-PHOSPHATE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsRuegenberg, S. / Horn, M. / Pichlo, C. / Allmeroth, K. / Baumann, U. / Denzel, M.S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research01GQ1423A Germany
European CommissionERC-2014-StG-640254-MetAGEn Germany
CitationJournal: Nat Commun / Year: 2020
Title: Loss of GFAT-1 feedback regulation activates the hexosamine pathway that modulates protein homeostasis.
Authors: Ruegenberg, S. / Horn, M. / Pichlo, C. / Allmeroth, K. / Baumann, U. / Denzel, M.S.
History
DepositionMar 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)155,9124
Polymers155,3922
Non-polymers5202
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer, light scattering, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-20 kcal/mol
Surface area47670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.022, 153.022, 167.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 77696.008 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis tris propane pH 9.0, 0.25 M Potassium sodium tartrate, 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: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.81 Å / Num. obs: 69161 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 20.61
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 6763 / CC1/2: 0.452

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Processing

Software
NameVersionClassification
PHENIX(dev_2499: ???)refinement
XDSJan 26, 2018data reduction
XDSJan 26, 2018data scaling
PHENIX(dev_2499: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R4E

6r4e


Resolution: 2.501→48.806 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 1936 2.8 %
Rwork0.1939 --
obs0.1945 69156 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→48.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10236 0 32 71 10339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310441
X-RAY DIFFRACTIONf_angle_d0.48714095
X-RAY DIFFRACTIONf_dihedral_angle_d12.5916337
X-RAY DIFFRACTIONf_chiral_restr0.0431613
X-RAY DIFFRACTIONf_plane_restr0.0021812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5014-2.5640.33871340.324671X-RAY DIFFRACTION98
2.564-2.63330.28431380.28274744X-RAY DIFFRACTION100
2.6333-2.71080.28461360.26464728X-RAY DIFFRACTION100
2.7108-2.79830.24381360.25824745X-RAY DIFFRACTION100
2.7983-2.89830.27671370.24524743X-RAY DIFFRACTION100
2.8983-3.01430.27421360.23564762X-RAY DIFFRACTION100
3.0143-3.15150.24531370.22954766X-RAY DIFFRACTION100
3.1515-3.31760.27281370.22124759X-RAY DIFFRACTION100
3.3176-3.52540.23291380.21674803X-RAY DIFFRACTION100
3.5254-3.79750.19931380.19234805X-RAY DIFFRACTION100
3.7975-4.17940.20151390.16314815X-RAY DIFFRACTION100
4.1794-4.78380.17051410.14754853X-RAY DIFFRACTION100
4.7838-6.02530.19081410.17534906X-RAY DIFFRACTION100
6.0253-48.81510.19971480.18215120X-RAY DIFFRACTION100
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)
14.2716-0.8999-0.54934.2295-0.30213.19930.0779-0.00430.0001-0.2084-0.1412-0.80950.23250.81640.04650.47220.11250.08890.68750.09310.61015.519954.157-73.9192
21.92420.61470.46011.90930.33580.91990.01160.1120.23540.0762-0.00280.2355-0.0667-0.0008-0.00110.47930.0299-0.02850.42960.0240.4818-13.078251.5894-38.8815
32.59650.1653-0.8433.0198-0.77340.53960.2713-0.7522-0.30031.4709-0.22820.1957-0.3319-0.3183-0.05571.932-0.2097-0.00951.61170.09110.9691-13.866334.37539.128
42.37490.64520.38372.23680.39431.0690.1843-0.1283-0.40350.4833-0.051-0.32940.22030.1768-0.12190.53490.0186-0.16520.3920.03540.50231.797630.0383-26.1014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 314 )
2X-RAY DIFFRACTION2chain 'A' and (resid 315 through 681 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 314 )
4X-RAY DIFFRACTION4chain 'B' and (resid 315 through 681 )

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