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- PDB-4amv: E.COLI GLUCOSAMINE-6P SYNTHASE IN COMPLEX WITH FRUCTOSE-6P -

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Basic information

Entry
Database: PDB / ID: 4amv
TitleE.COLI GLUCOSAMINE-6P SYNTHASE IN COMPLEX WITH FRUCTOSE-6P
ComponentsGLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
KeywordsTRANSFERASE / AMMONIA CHANNELING / GLUCOSAMINE 6- PHOSPHATE SYNTHASE / N TERMINAL NUCLEOPHILE / GLUTAMINE AMIDOTRANSFERASE
Function / homology
Function and homology information


glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / carbohydrate metabolic process / 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 / Glucose-6-phosphate isomerase like protein; domain 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FRUCTOSE -6-PHOSPHATE / Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMouilleron, S. / Golinelli-Pimpaneau, B.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Glutamine Binding Opens the Ammonia Channel and Activates Glucosamine-6P Synthase
Authors: Mouilleron, S. / Badet-Denisot, M.A. / Golinelli-Pimpaneau, B.
#1: Journal: Protein Sci. / Year: 2007
Title: Domain Motions of Glucosamine-6P Synthase: Comparison of the Anisotropic Displacements in the Crystals and the Catalytic Hinge-Bending Rotation.
Authors: Mouilleron, S. / Golinelli-Pimpaneau, B.
#2: Journal: J.Mol.Biol. / Year: 2008
Title: Ordering of C-Terminal Loop and Glutaminase Domains of Glucosamine-6-Phosphate Synthase Promotes Sugar Ring Opening and Formation of the Ammonia Channel.
Authors: Mouilleron, S. / Badet-Denisot, M. / Golinelli-Pimpaneau, B.
#3: Journal: Arch.Biochem.Biophys. / Year: 2011
Title: Dynamics of Glucosamine-6-Phosphate Synthase Catalysis.
Authors: Mouilleron, S. / Badet-Denisot, M. / Badet, B. / Golinelli-Pimpaneau, B.
History
DepositionMar 14, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionApr 24, 2013ID: 2BPL
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
B: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
C: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,6286
Polymers200,8483
Non-polymers7803
Water12,502694
1
A: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
hetero molecules

A: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4194
Polymers133,8982
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7200 Å2
ΔGint-19.1 kcal/mol
Surface area41780 Å2
MethodPISA
2
B: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
C: GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4194
Polymers133,8982
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-21.3 kcal/mol
Surface area41470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.197, 109.677, 176.332
Angle α, β, γ (deg.)90.00, 97.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2088-

HOH

21A-2250-

HOH

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Components

#1: Protein GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMER IZING] / D-FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE / GFAT / GLUCOSAMINE- 6-PHOSPHATE SYNTHASE / ...D-FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE / GFAT / GLUCOSAMINE- 6-PHOSPHATE SYNTHASE / HEXOSEPHOSPHATE AMINOTRANSFERASE / L-GLUTAMINE- D-FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE


Mass: 66949.195 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PMA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101
References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing)
#2: Chemical ChemComp-F6R / FRUCTOSE -6-PHOSPHATE / Fructose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 151822

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.8 % / Description: NONE
Crystal growpH: 7.5
Details: 3% PEG 400, 0.1 M HEPES PH 7.5, 0.8 M LICL, 0.01 M FRUCTOSE-6P

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 151822 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.45 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.75
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.62 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JXA CHAIN A

1jxa


Resolution: 2.05→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.238 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23992 7769 5 %RANDOM
Rwork0.2058 ---
obs0.20755 146279 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.557 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å21.02 Å2
2---0.39 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.05→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13483 0 48 694 14225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01913748
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.96718650
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34651821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26124.26561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.531152228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2611583
X-RAY DIFFRACTIONr_chiral_restr0.1710.22165
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110350
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 553 -
Rwork0.335 10277 -
obs--97.3 %
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)
13.04560.22460.0062.3031-0.5423.59270.0049-0.4453-0.17290.3452-0.0477-0.0620.08730.09650.04280.0835-0.0635-0.05130.31950.03740.291228.69723.493994.8561
21.40940.0415-0.11841.44350.32231.2674-0.12220.1727-0.0958-0.18390.1261-0.1273-0.03310.1063-0.00380.0355-0.04840.02210.1731-0.02850.208-2.3707-2.197875.5623
35.37871.3803-1.48175.0146-0.69656.9424-0.20380.0397-0.4133-0.06150.05570.59771.8849-0.95210.1482.5331-0.44270.04770.3657-0.21960.346450.2601-53.482411.4685
40.8456-0.1277-0.63552.28541.62795.84180.0450.27060.171-0.48660.0921-0.25030.8815-0.1208-0.1371.0107-0.1630.04940.3167-0.00480.249856.3808-19.391923.22
51.80870.628-0.66733.1523-0.26863.3238-0.02710.08840.0912-0.32690.1575-0.14490.2015-0.2224-0.13040.1027-0.1127-0.02510.2288-0.06860.255850.57119.456361.5068
61.3471-0.3128-0.78532.25880.59293.2221-0.08180.2289-0.0142-0.2046-0.09360.54060.8856-0.96550.17540.7508-0.4622-0.09260.6391-0.08520.351835.8207-19.272443.6147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 234
2X-RAY DIFFRACTION2A238 - 608
3X-RAY DIFFRACTION2A1609
4X-RAY DIFFRACTION3B1 - 234
5X-RAY DIFFRACTION4B238 - 608
6X-RAY DIFFRACTION4B1609
7X-RAY DIFFRACTION5C1 - 234
8X-RAY DIFFRACTION6C238 - 608
9X-RAY DIFFRACTION6C1609

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