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- PDB-1i3k: MOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-R... -

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Basic information

Entry
Database: PDB / ID: 1i3k
TitleMOLECULAR BASIS FOR SEVERE EPIMERASE-DEFICIENCY GALACTOSEMIA: X-RAY STRUCTURE OF THE HUMAN V94M-SUBSTITUTED UDP-GALACTOSE 4-EPIMERASE
ComponentsUDP-GLUCOSE 4-EPIMERASE
KeywordsISOMERASE / Galactosemia epimerase short-chain dehydrogenase
Function / homology
Function and homology information


Defective GALE causes EDG / UDP-N-acetylglucosamine 4-epimerase activity / UDP-N-acetylglucosamine 4-epimerase / galactose catabolic process / Galactose catabolism / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
UDP-glucose 4-epimerase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsThoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Molecular basis for severe epimerase deficiency galactosemia. X-ray structure of the human V94m-substituted UDP-galactose 4-epimerase.
Authors: Thoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / Holden, H.M.
History
DepositionFeb 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-GLUCOSE 4-EPIMERASE
B: UDP-GLUCOSE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,58114
Polymers76,7692
Non-polymers2,81212
Water17,601977
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-86 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.100, 89.900, 96.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer comprised of chains A & B

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-GLUCOSE 4-EPIMERASE / UDP-GALACTOSE 4-EPIMERASE


Mass: 38384.727 Da / Num. of mol.: 2 / Mutation: V94M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGALE / Plasmid: PPIC3.5KHGALE / Production host: Pichia pastoris (fungus) / References: UniProt: Q14376, UDP-glucose 4-epimerase

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Non-polymers , 6 types, 989 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 977 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 278 K / Method: batch / pH: 6
Details: PEG-3400, MES, sodium chloride, magnesium chloride, pH 6, batch, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: batch method / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMMES11
28-9 %(w/v)PEG340011
375 mM11MgCl2
415 mg/mlprotein11
55 mMNADH11
620 mMUDP-sugars11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 108944 / Num. obs: 108944 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 41
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.5 / Num. unique all: 10333 / % possible all: 95.3
Reflection
*PLUS
Num. obs: 10333 / Num. measured all: 108944
Reflection shell
*PLUS
% possible obs: 95.3 %

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Processing

Software
NameClassification
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1EK6

1ek6


Resolution: 1.5→50 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 10687 -RANDOM
Rwork0.174 ---
all0.175 108668 --
obs0.175 108668 99.1 %-
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 178 977 6568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_bond_d0.01
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.175 / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.1

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