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- PDB-6r4i: Crystal structure of human GFAT-1 G461E -

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Basic information

Entry
Database: PDB / ID: 6r4i
TitleCrystal structure of human GFAT-1 G461E
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 / GLUTAMIC ACID / Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.586 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
Item: _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)156,2045
Polymers155,5362
Non-polymers6673
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer, light scattering, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-25 kcal/mol
Surface area48550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.753, 152.753, 165.988
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: 77768.070 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.: 64 / 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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis tris propane pH 8.5, 0.35 M Potassium sodium tartrate, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.586→48.68 Å / Num. obs: 61581 / % possible obs: 99.6 % / Redundancy: 10 % / CC1/2: 0.999 / Net I/σ(I): 17.49
Reflection shellResolution: 2.586→2.68 Å / Num. unique obs: 5916 / CC1/2: 0.556

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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: 2.586→48.679 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.54
RfactorNum. reflection% reflection
Rfree0.2189 1967 3.19 %
Rwork0.1917 --
obs0.1925 61567 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.586→48.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10357 0 42 64 10463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210573
X-RAY DIFFRACTIONf_angle_d0.44414272
X-RAY DIFFRACTIONf_dihedral_angle_d12.4666431
X-RAY DIFFRACTIONf_chiral_restr0.0421636
X-RAY DIFFRACTIONf_plane_restr0.0021833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5859-2.65060.31161250.29664036X-RAY DIFFRACTION96
2.6506-2.72220.31781280.27054222X-RAY DIFFRACTION100
2.7222-2.80230.31551380.26714204X-RAY DIFFRACTION100
2.8023-2.89280.29531580.24744213X-RAY DIFFRACTION100
2.8928-2.99610.26781250.25594254X-RAY DIFFRACTION100
2.9961-3.11610.30291450.23644199X-RAY DIFFRACTION100
3.1161-3.25790.24251430.21874235X-RAY DIFFRACTION100
3.2579-3.42960.2541380.2154246X-RAY DIFFRACTION100
3.4296-3.64440.19791490.19454243X-RAY DIFFRACTION100
3.6444-3.92570.18971370.1694275X-RAY DIFFRACTION100
3.9257-4.32050.17751390.15494252X-RAY DIFFRACTION99
4.3205-4.94520.18911470.14824313X-RAY DIFFRACTION100
4.9452-6.22830.22441450.19014358X-RAY DIFFRACTION100
6.2283-48.68740.20151500.18474550X-RAY DIFFRACTION99
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)
13.2066-0.461-0.17722.32240.15922.49010.04720.0512-0.0228-0.2231-0.0619-0.75310.21020.74540.00410.48440.09280.09970.69410.07730.65955.488853.7534-73.9193
21.8410.52980.26121.87350.30531.19290.00690.09420.18050.11710.02870.1464-0.1217-0.0144-0.02890.40580.0306-0.01060.39150.03240.4281-12.737551.6782-38.5387
30.3364-0.1206-0.37772.201-0.63090.45860.2026-0.62950.02811.3983-0.3360.3732-0.8338-0.29340.14412.2713-0.1726-0.07232.24680.11421.3915-13.535634.91589.6083
42.36260.66140.39291.76580.36451.39660.1614-0.1298-0.36990.4834-0.0542-0.34450.19170.2018-0.1010.55030.0167-0.14380.36710.03190.53392.114330.1361-25.9421
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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