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- PDB-1ne7: HUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOL... -

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Basic information

Entry
Database: PDB / ID: 1ne7
TitleHUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOLUTION COMPLEXED WITH N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AND 2-DEOXY-2-AMINO-GLUCITOL-6-PHOSPHATE
ComponentsGlucosamine-6-phosphate isomerase
KeywordsHYDROLASE / V-TYPE LIKE ALLOSTERIC ENZYME / CONFORMATIONAL DISORDER / CONFORMATIONAL DIFFERENCES
Function / homology
Function and homology information


glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / Glycolysis / single fertilization / isomerase activity / generation of precursor metabolites and energy ...glucosamine catabolic process / glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / Glycolysis / single fertilization / isomerase activity / generation of precursor metabolites and energy / carbohydrate metabolic process / extracellular exosome / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Glucosamine-6-phosphate isomerase, conserved site / Glucosamine/galactosamine-6-phosphate isomerases signature. / Glucosamine-6-phosphate isomerase / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
trehalose / Chem-16G / 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE / Glucosamine-6-phosphate deaminase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsArreola, R. / Valderrama, B. / Morante, M.L. / Horjales, E.
Citation
Journal: Febs Lett. / Year: 2003
Title: Two mammalian glucosamine-6-phosphate deaminases: a structural and genetic study.
Authors: Arreola, R. / Valderrama, B. / Morante, M.L. / Horjales, E.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1998
Title: Glucosamine-6-phosphate deaminase from beef kidney is an allosteric system of the V-type.
Authors: Lara-Lemus, R. / Calcagno, M.L.
#2: Journal: Structure / Year: 1995
Title: Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 A resolution.
Authors: Oliva, G. / Fontes, M.R. / Garratt, R.C. / Altamirano, M.M. / Calcagno, M.L. / Horjales, E.
History
DepositionDec 10, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionSep 23, 2003ID: 1D9T
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 14, 2020Group: Structure summary / Category: chem_comp / pdbx_molecule_features / Item: _chem_comp.pdbx_synonyms
Revision 2.2Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN THE LIGANDS SO4 AND AGP ARE IN ALTERNATE POSITIONS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosamine-6-phosphate isomerase
B: Glucosamine-6-phosphate isomerase
C: Glucosamine-6-phosphate isomerase
D: Glucosamine-6-phosphate isomerase
E: Glucosamine-6-phosphate isomerase
F: Glucosamine-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,37531
Polymers196,2756
Non-polymers6,10025
Water39,5252194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24290 Å2
ΔGint-182 kcal/mol
Surface area59100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.877, 110.892, 180.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the hexamer in the asymmetric unit reported in this entry. Chains: A, B, C, D, E & F.

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glucosamine-6-phosphate isomerase / Glucosamine-6-phosphate deaminase / GNPDA / GlcN6P deaminase / Oscillin


Mass: 32712.506 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNPI OR HLN OR KIAA0060 / Production host: Escherichia coli (E. coli)
References: UniProt: P46926, glucosamine-6-phosphate deaminase

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Sugars , 2 types, 12 molecules

#2: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-16G / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / N-acetyl-6-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 2207 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-AGP / 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE


Mass: 261.167 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H16NO8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2194 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.68 M ammonium sulphate, 10 mM N-acetyl-glucosamine-6-phosphate and 0.1 mM 2-deoxy-2-amino D-glucitol 6-phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.68 Mammonium sulfate1reservoir
310 mMN-acetyl-glucosamine-6-phosphate1reservoir
40.1 mM2-deoxy-2-amino-D-glucitol-6-phosphate1reservoirpH7.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78 Å / Relative weight: 1
ReflectionResolution: 1.75→19.97 Å / Num. all: 221759 / Num. obs: 209143 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.052 / Net I/σ(I): 9.9
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 32182 / Rsym value: 0.224 / % possible all: 95.8
Reflection
*PLUS
Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 96.8 % / Rmerge(I) obs: 0.224

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DEA

1dea


Resolution: 1.75→19.97 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 20802 9.9 %RANDOM
Rwork0.193 ---
all0.1954 221759 --
obs0.1954 209143 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.2697 Å2 / ksol: 0.376291 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å20 Å2
2--6.35 Å20 Å2
3----4.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13436 0 383 2194 16013
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 1.75→1.76 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.216 436 10 %
Rwork0.1929 31921 -
obs-4218 96.8 %
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Lowest resolution: 1.86 Å / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.223

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