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- PDB-6r4e: Crystal structure of human GFAT-1 in complex with Glucose-6-Phosp... -

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Basic information

Entry
Database: PDB / ID: 6r4e
TitleCrystal structure of human GFAT-1 in complex with Glucose-6-Phosphate and L-Glu
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: 2.353 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
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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)156,2195
Polymers155,5522
Non-polymers6673
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer, light scattering, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-23 kcal/mol
Surface area49170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.847, 153.847, 166.292
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: 77775.984 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 natural 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.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 61.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis tris propane pH 8.25, 0.4 M Potassium sodium tartrate, 20 % PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→40.134 Å / Num. obs: 82721 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 18.1
Reflection shellResolution: 2.35→2.44 Å / Num. unique obs: 7933 / CC1/2: 0.686

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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: 2ZJ3

2zj3


Resolution: 2.353→40.134 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 22.18
RfactorNum. reflection% reflection
Rfree0.2097 1991 2.41 %
Rwork0.1742 --
obs0.1751 82715 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.353→40.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10430 0 42 80 10552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210646
X-RAY DIFFRACTIONf_angle_d0.45214376
X-RAY DIFFRACTIONf_dihedral_angle_d12.426471
X-RAY DIFFRACTIONf_chiral_restr0.0421648
X-RAY DIFFRACTIONf_plane_restr0.0021846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.353-2.41190.31051390.25945462X-RAY DIFFRACTION96
2.4119-2.47710.29381330.24345695X-RAY DIFFRACTION100
2.4771-2.550.30641390.23255701X-RAY DIFFRACTION100
2.55-2.63220.26821560.22245717X-RAY DIFFRACTION100
2.6322-2.72630.25561330.21945717X-RAY DIFFRACTION100
2.7263-2.83540.29391260.2155731X-RAY DIFFRACTION100
2.8354-2.96440.2511650.19925734X-RAY DIFFRACTION100
2.9644-3.12070.24131310.20325736X-RAY DIFFRACTION100
3.1207-3.31610.23291390.20755770X-RAY DIFFRACTION100
3.3161-3.5720.21041470.1955789X-RAY DIFFRACTION100
3.572-3.93120.20171430.16365793X-RAY DIFFRACTION100
3.9312-4.49940.1731430.14515839X-RAY DIFFRACTION100
4.4994-5.66620.16551410.14275901X-RAY DIFFRACTION100
5.6662-40.13930.20341560.16076139X-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)
12.2452-0.6507-0.16872.0419-0.32632.2873-0.023-0.0577-0.0215-0.1928-0.055-0.65910.22820.6907-0.00390.50990.11450.13040.81410.12110.80829.254754.5257-73.8139
21.46880.47480.32951.33980.0811.02960.00830.14030.18170.07450.02060.1644-0.06840.000800.48730.0249-0.00950.45960.01810.5219-12.721551.9181-38.4676
31.0052-0.2933-0.21790.52190.15670.40910.1223-0.6742-0.23820.9241-0.17050.1823-0.1176-0.2616-0.00011.7759-0.25640.04891.50780.04030.9218-13.53938.365310.1607
41.97950.45510.29541.60530.18690.84510.1268-0.08-0.30460.3881-0.055-0.24750.14150.1248-00.59210.0147-0.15230.47560.02710.55952.314330.2282-26.0456
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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