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- PDB-3lxa: Interconversion of Human Lysosomal Enzyme Specificities -

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Basic information

Entry
Database: PDB / ID: 3lxa
TitleInterconversion of Human Lysosomal Enzyme Specificities
ComponentsAlpha-galactosidase A
KeywordsHYDROLASE / GLYCOPROTEIN / CARBOHYDRATE-BINDING PROTEIN / GLYCOSIDASE / LYSOSOMAL ENZYME / (BETA/ALPHA)8 BARREL / ENZYME INTERCONVERSION / Disease mutation / Disulfide bond / Lysosome
Function / homology
Function and homology information


negative regulation of nitric-oxide synthase activity / glycosylceramide catabolic process / alpha-galactosidase / glycosphingolipid catabolic process / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism / catalytic activity ...negative regulation of nitric-oxide synthase activity / glycosylceramide catabolic process / alpha-galactosidase / glycosphingolipid catabolic process / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism / catalytic activity / lysosomal lumen / azurophil granule lumen / lysosome / hydrolase activity / signaling receptor binding / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / membrane / cytoplasm
Similarity search - Function
Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel ...Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-D-galactopyranose / Alpha-galactosidase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 3.04 Å
AuthorsTomasic, I.B. / Metcalf, M.C. / Guce, A.I. / Clark, N.E. / Garman, S.C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Interconversion of the specificities of human lysosomal enzymes associated with Fabry and Schindler diseases.
Authors: Tomasic, I.B. / Metcalf, M.C. / Guce, A.I. / Clark, N.E. / Garman, S.C.
History
DepositionFeb 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.3Oct 9, 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: Alpha-galactosidase A
B: Alpha-galactosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,58512
Polymers92,2792
Non-polymers3,30610
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint51 kcal/mol
Surface area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.241, 104.959, 181.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUARGARGAA32 - 1001 - 69
211LEULEUARGARGBB32 - 1001 - 69
121LEULEUILEILEAA106 - 11775 - 86
221LEULEUILEILEBB106 - 11775 - 86
131GLNGLNALAALAAA119 - 15688 - 125
231GLNGLNALAALABB119 - 15688 - 125
141GLYGLYMETMETAA163 - 208132 - 177
241GLYGLYMETMETBB163 - 208132 - 177
151PROPROASNASNAA214 - 228183 - 197
251PROPROASNASNBB214 - 228183 - 197
161ALAALAASPASPAA230 - 244199 - 213
261ALAALAASPASPBB230 - 244199 - 213
171ILEILEGLYGLYAA253 - 328222 - 297
271ILEILEGLYGLYBB253 - 328222 - 297
112TYRTYRLEULEUAA329 - 344298 - 313
212TYRTYRLEULEUBB329 - 344298 - 313
122ALAALACYSCYSAA348 - 378317 - 347
222ALAALACYSCYSBB348 - 378317 - 347
132ILEILEARGARGAA384 - 392353 - 361
232ILEILEARGARGBB384 - 392353 - 361
142TRPTRPMETMETAA399 - 421368 - 390
242TRPTRPMETMETBB399 - 421368 - 390

NCS ensembles :
ID
1
2

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Components

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Protein / Non-polymers , 2 types, 38 molecules AB

#1: Protein Alpha-galactosidase A / Alpha-D-galactoside galactohydrolase / Alpha-D-galactosidase A / Melibiase


Mass: 46139.301 Da / Num. of mol.: 2 / Fragment: UNP residues 32-429 / Mutation: E203S L206A
Source method: isolated from a genetically manipulated source
Details: Selected with blastocidin / Source: (gene. exp.) Homo sapiens (human) / Gene: GLA / Plasmid: pIB/V5-His-TOPO TA / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HI-FIVE / References: UniProt: P06280, alpha-galactosidase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 10 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2009 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 23638 / Num. obs: 23638 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.271 / Χ2: 1.107 / Net I/σ(I): 7.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2309 / Rsym value: 0.851 / Χ2: 1.081 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3HG3

3hg3


Resolution: 3.04→49.63 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.858 / Occupancy max: 1 / Occupancy min: 1 / SU B: 37.701 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1128 5 %RANDOM
Rwork0.214 ---
obs0.216 22400 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.46 Å2 / Biso mean: 34.52 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 3.04→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6303 0 218 36 6557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226718
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9739145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02524.277318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.716151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8361538
X-RAY DIFFRACTIONr_chiral_restr0.0880.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215076
X-RAY DIFFRACTIONr_mcbond_it1.43663919
X-RAY DIFFRACTIONr_mcangle_it2.76896278
X-RAY DIFFRACTIONr_scbond_it3.57662799
X-RAY DIFFRACTIONr_scangle_it5.89592867
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12142TIGHT POSITIONAL0.090.05
12142TIGHT THERMAL0.050.5
2627TIGHT POSITIONAL0.140.05
2627TIGHT THERMAL0.050.5
LS refinement shellResolution: 3.039→3.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 63 -
Rwork0.325 1506 -
all-1569 -
obs--94.23 %
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)
10.25890.00270.20650.4705-0.18641.38880.01970.00950.0325-0.0012-0.01930.01560.00420.0567-0.00030.00260.0027-0.00370.0078-0.01380.04087.2022-4.140520.1429
21.068-0.1496-0.29380.4395-0.33410.73710.1204-0.0119-0.03110.0110.04140.07020.1928-0.1412-0.16180.2178-0.0799-0.08230.03850.04140.0457-1.0388-18.482846.0593
30.3183-0.0272-0.12860.0927-0.23390.7293-0.0166-0.03670.03020.02550.03690.0113-0.0618-0.0717-0.02030.02080.0132-0.01240.0162-0.00870.054221.89495.188564.7355
41.2107-0.0147-0.26981.3952-0.3540.2744-0.01510.10880.25620.0270.014-0.1169-0.053-0.05320.00120.02080.0091-0.0170.01510.0160.0735.99812.31138.2526
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 328
2X-RAY DIFFRACTION2A329 - 426
3X-RAY DIFFRACTION3B32 - 328
4X-RAY DIFFRACTION4B329 - 425

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