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- PDB-6svq: Crystal structure of human GFAT-1 G461E after UDP-GlcNAc soaking -

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Basic information

Entry
Database: PDB / ID: 6svq
TitleCrystal structure of human GFAT-1 G461E after UDP-GlcNAc soaking
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 / 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: 2.717 Å
AuthorsRuegenberg, S. / Horn, M. / Pichlo, C. / Allmeroth, K. / 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
European UnioniNEXT, Horizon 2020 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
DepositionSep 18, 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
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer, light scattering, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-22 kcal/mol
Surface area48750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.453, 152.453, 164.904
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


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.: 10 / 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: 3.27 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis tris propane pH 8.75, 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: 2.717→48.969 Å / Num. obs: 52752 / % possible obs: 99.7 % / Redundancy: 8.8 % / CC1/2: 0.999 / Net I/σ(I): 16.86
Reflection shellResolution: 2.717→2.81 Å / Num. unique obs: 5146 / CC1/2: 0.549

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Processing

Software
NameVersionClassification
PHENIXdev_2499refinement
PDB_EXTRACT3.25data extraction
XDSJan 26, 2018data reduction
XDSJan 26, 2018data scaling
PHENIXdev_2499phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R4E

6r4e


Resolution: 2.717→48.969 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.1
RfactorNum. reflection% reflection
Rfree0.2336 1940 3.68 %
Rwork0.2048 --
obs0.2059 52739 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 551.93 Å2 / Biso mean: 125.9879 Å2 / Biso min: 39.75 Å2
Refinement stepCycle: final / Resolution: 2.717→48.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10218 0 76 10 10304
Biso mean--75.44 53.11 -
Num. residues----1291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210434
X-RAY DIFFRACTIONf_angle_d0.4414084
X-RAY DIFFRACTIONf_chiral_restr0.0421609
X-RAY DIFFRACTIONf_plane_restr0.0021811
X-RAY DIFFRACTIONf_dihedral_angle_d12.436341
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.717-2.78440.31191290.3105350398
2.7844-2.85970.32331520.28943563100
2.8597-2.94390.26211240.27253614100
2.9439-3.03890.32041450.28393583100
3.0389-3.14750.28571390.26193562100
3.1475-3.27350.28011380.24293620100
3.2735-3.42240.30191370.23353598100
3.4224-3.60280.27011300.22663629100
3.6028-3.82840.23131520.18833627100
3.8284-4.12390.19051360.17323637100
4.1239-4.53860.17831380.1647357298
4.5386-5.19470.16021360.15833691100
5.1947-6.54240.27931380.21693719100
6.5424-48.9690.22871460.1992388199
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)
13.35370.6396-0.05823.9154-0.1512.7185-0.09580.296-0.6775-0.05530.04860.05770.6499-0.22770.04290.7238-0.11370.09280.491-0.1260.671953.356146.9203-32.7216
22.0969-0.6850.15891.8058-0.42011.11610.0351-0.18140.2363-0.09470.0053-0.2193-0.0610.1297-0.02190.4035-0.04050.02110.45610.0050.45551.4758165.53142.9484
30.01140.0810.07750.36790.35180.3164-0.1059-0.85860.440.75570.31330.5286-0.19060.1028-0.23942.19670.19440.21782.14230.06511.859935.3773165.826251.1917
42.2044-0.71130.18482.6346-0.43841.1245-0.0614-0.4865-0.34960.18510.17840.39480.1788-0.1663-0.10590.3903-0.00190.02730.57090.14910.54429.8972149.86915.1464
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 679 )A315 - 679
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 314 )B2 - 314
4X-RAY DIFFRACTION4chain 'B' and (resid 315 through 678 )B315 - 678

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