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

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Basic information

Entry
Database: PDB / ID: 3lxc
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-galactosidase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 2.3Nov 27, 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)95,88410
Polymers92,2792
Non-polymers3,6058
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint50 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.947, 139.492, 182.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B
111A
211B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUASPASPAA32 - 1011 - 70
21LEULEUASPASPBB32 - 1011 - 70
12ALAALAPHEPHEAA108 - 11377 - 82
22ALAALAPHEPHEBB108 - 11377 - 82
13GLNGLNASPASPAA119 - 15388 - 122
23GLNGLNASPASPBB119 - 15388 - 122
14ASPASPALAALAAA155 - 160124 - 129
24ASPASPALAALABB155 - 160124 - 129
15TRPTRPMETMETAA162 - 208131 - 177
25TRPTRPMETMETBB162 - 208131 - 177
16TYRTYRSERSERAA216 - 247185 - 216
26TYRTYRSERSERBB216 - 247185 - 216
17ILEILEARGARGAA253 - 342222 - 311
27ILEILEARGARGBB253 - 342222 - 311
18ALAALAILEILEAA348 - 367317 - 336
28ALAALAILEILEBB348 - 367317 - 336
19ALAALALYSLYSAA381 - 393350 - 362
29ALAALALYSLYSBB381 - 393350 - 362
110TYRTYRGLUGLUAA397 - 398366 - 367
210TYRTYRGLUGLUBB397 - 398366 - 367
111LEULEUTHRTHRAA403 - 420372 - 389
211LEULEUTHRTHRBB403 - 420372 - 389

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

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Components

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Protein , 1 types, 2 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

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Sugars , 4 types, 6 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 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)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4/a3-b1_a4-c1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 2
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

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Non-polymers , 2 types, 554 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.36 %
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: APS / Beamline: 24-ID-C / Wavelength: 1.07188 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2009 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07188 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 47535 / Num. obs: 47535 / % possible obs: 98.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.153 / Χ2: 1.457 / Net I/σ(I): 12.3
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 2 / Num. unique all: 2335 / Rsym value: 0.862 / Χ2: 1.066 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HG3

3hg3


Resolution: 2.35→43.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 1 / SU B: 18.709 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2377 5 %RANDOM
Rwork0.184 ---
obs0.186 47496 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 130.42 Å2 / Biso mean: 45.302 Å2 / Biso min: 7.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.35→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6241 0 239 552 7032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216680
X-RAY DIFFRACTIONr_bond_other_d0.0010.024517
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9769099
X-RAY DIFFRACTIONr_angle_other_deg0.8133.00410882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55424.259317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.522151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3851538
X-RAY DIFFRACTIONr_chiral_restr0.0660.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021351
X-RAY DIFFRACTIONr_mcbond_it2.8071.53879
X-RAY DIFFRACTIONr_mcbond_other0.9491.51584
X-RAY DIFFRACTIONr_mcangle_it4.61226214
X-RAY DIFFRACTIONr_scbond_it7.27732801
X-RAY DIFFRACTIONr_scangle_it10.1784.52885
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1972MEDIUM POSITIONAL0.170.5
1972MEDIUM THERMAL0.652
292MEDIUM POSITIONAL0.280.5
292MEDIUM THERMAL0.752
3447MEDIUM POSITIONAL0.150.5
3447MEDIUM THERMAL0.692
471MEDIUM POSITIONAL0.410.5
471MEDIUM THERMAL0.782
5631MEDIUM POSITIONAL0.260.5
5631MEDIUM THERMAL0.732
6479MEDIUM POSITIONAL0.240.5
6479MEDIUM THERMAL0.772
71187MEDIUM POSITIONAL0.240.5
71187MEDIUM THERMAL0.782
8266MEDIUM POSITIONAL0.130.5
8266MEDIUM THERMAL0.732
9188MEDIUM POSITIONAL0.140.5
9188MEDIUM THERMAL0.512
1035MEDIUM POSITIONAL0.230.5
1035MEDIUM THERMAL0.582
11230MEDIUM POSITIONAL0.250.5
11230MEDIUM THERMAL0.572
LS refinement shellResolution: 2.347→2.408 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 165 -
Rwork0.398 3162 -
all-3327 -
obs--94.95 %
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)
10.3153-0.0436-0.04330.01220.04630.6962-0.0083-0.01090.01320.00380.01510.00410.0524-0.0845-0.00690.0549-0.03430.01150.06030.00380.094424.93927.205959.5003
20.5701-0.4645-0.21990.9874-0.49530.89580.00390.1135-0.0248-0.1038-0.0421-0.01730.2196-0.16160.03820.2313-0.1066-0.01270.0806-0.01860.056225.489311.173433.0786
30.2204-0.1654-0.10370.17050.17761.2060.0291-0.00360.008-0.06470.0103-0.0036-0.02530.0257-0.03940.0499-0.0297-0.00660.070.00550.08821.09442.980714.1444
40.425-0.54660.02961.6525-1.17031.4247-0.1083-0.05780.03470.20340.2198-0.0172-0.1585-0.2003-0.11150.10910.04270.01980.04850.00090.086812.730556.490240.6213
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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