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- PDB-6r4j: Crystal structure of human GFAT-1 G451E in complex with UDP-GlcNAc -

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Basic information

Entry
Database: PDB / ID: 6r4j
TitleCrystal structure of human GFAT-1 G451E in complex with UDP-GlcNAc
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 / fructose 6-phosphate metabolic process ...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 / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine 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 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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)157,4679
Polymers155,5362
Non-polymers1,9317
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer, light scattering, tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-48 kcal/mol
Surface area48110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.227, 153.227, 162.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 133 molecules

#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-G6Q / GLUCOSE-6-PHOSPHATE


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


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


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis tris propane pH 9.0, 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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→48.73 Å / Num. obs: 74011 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 18.36
Reflection shellResolution: 2.42→2.51 Å / Num. unique obs: 7226 / CC1/2: 0.599

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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: 2.42→48.727 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 1991 2.69 %
Rwork0.1941 --
obs0.1949 74006 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→48.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10322 0 122 126 10570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210620
X-RAY DIFFRACTIONf_angle_d0.44414347
X-RAY DIFFRACTIONf_dihedral_angle_d12.4486414
X-RAY DIFFRACTIONf_chiral_restr0.0421646
X-RAY DIFFRACTIONf_plane_restr0.0021831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4201-2.48070.31281410.27965035X-RAY DIFFRACTION99
2.4807-2.54770.27031390.26445041X-RAY DIFFRACTION100
2.5477-2.62270.28971390.24785065X-RAY DIFFRACTION100
2.6227-2.70730.27271390.23885103X-RAY DIFFRACTION100
2.7073-2.80410.27651370.2335081X-RAY DIFFRACTION100
2.8041-2.91640.31771500.23425093X-RAY DIFFRACTION100
2.9164-3.04910.24591420.21925110X-RAY DIFFRACTION100
3.0491-3.20980.26251340.22085130X-RAY DIFFRACTION100
3.2098-3.41080.24151430.2135103X-RAY DIFFRACTION100
3.4108-3.67410.21661450.19525141X-RAY DIFFRACTION100
3.6741-4.04370.21831410.17165181X-RAY DIFFRACTION100
4.0437-4.62840.1661420.15185207X-RAY DIFFRACTION100
4.6284-5.82980.17791460.17015241X-RAY DIFFRACTION100
5.8298-48.73650.21471530.18275484X-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)
13.27050.2986-0.10053.02660.38472.3745-0.10590.2064-0.5873-0.15830.12140.07570.6036-0.2294-0.03080.5525-0.10820.03710.3623-0.0480.392753.2283-4.9683-34.0101
21.3216-0.41250.05151.244-0.29650.8001-0.0306-0.08410.20890.03980.0268-0.1784-0.02920.1270.01150.3114-0.0264-0.00620.3629-0.00050.364951.103412.36652.1471
31.8637-0.14070.52083.0601-0.16491.7571-0.2714-0.83590.03031.24540.1849-0.0623-0.56420.14470.06221.62920.1213-0.0261.4647-0.10120.870638.318711.928950.7479
41.5399-0.40510.091.6632-0.08260.8719-0.0509-0.281-0.1530.19190.11780.32060.1467-0.1204-0.06480.37040.00560.04570.42790.06670.415229.7886-3.240814.719
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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