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- PDB-3lpo: Crystal structure of the N-terminal domain of sucrase-isomaltase -

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Basic information

Entry
Database: PDB / ID: 3lpo
TitleCrystal structure of the N-terminal domain of sucrase-isomaltase
ComponentsSucrase-isomaltase
KeywordsHYDROLASE / Glycoside hydrolase family 31 / isomaltase / alpha-glucosidase / Cell membrane / Disease mutation / Disulfide bond / Glycoprotein / Glycosidase / Membrane / Multifunctional enzyme / Polymorphism / Signal-anchor / Sulfation / Transmembrane
Function / homology
Function and homology information


sucrose alpha-glucosidase / Intestinal saccharidase deficiencies / sucrose alpha-glucosidase activity / sucrose catabolic process / oligo-1,6-glucosidase / oligo-1,6-glucosidase activity / alpha-1,4-glucosidase activity / polysaccharide digestion / Digestion of dietary carbohydrate / brush border ...sucrose alpha-glucosidase / Intestinal saccharidase deficiencies / sucrose alpha-glucosidase activity / sucrose catabolic process / oligo-1,6-glucosidase / oligo-1,6-glucosidase activity / alpha-1,4-glucosidase activity / polysaccharide digestion / Digestion of dietary carbohydrate / brush border / carbohydrate binding / apical plasma membrane / Golgi apparatus / extracellular exosome / plasma membrane
Similarity search - Function
: / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain ...: / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / glycosyl hydrolase (family 31) / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Few Secondary Structures / Irregular / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sucrase-isomaltase, intestinal
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsSim, L. / Rose, D.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis for substrate selectivity in human maltase-glucoamylase and sucrase-isomaltase N-terminal domains.
Authors: Sim, L. / Willemsma, C. / Mohan, S. / Naim, H.Y. / Pinto, B.M. / Rose, D.R.
History
DepositionFeb 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification ..._pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_close_contact / 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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sucrase-isomaltase
B: Sucrase-isomaltase
C: Sucrase-isomaltase
D: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,24513
Polymers411,4694
Non-polymers3,7769
Water0
1
A: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4244
Polymers102,8671
Non-polymers1,5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0882
Polymers102,8671
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4244
Polymers102,8671
Non-polymers1,5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sucrase-isomaltase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3103
Polymers102,8671
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.344, 172.586, 343.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A28 - 65
2111B28 - 65
3111C28 - 65
4111D28 - 65
1211A67 - 898
2211B67 - 898
3211C67 - 898
4211D67 - 898

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Components

#1: Protein
Sucrase-isomaltase / / Sucrase / Isomaltase


Mass: 102867.148 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SI / Plasmid: pMT-TEVA / Cell (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14410, oligo-1,6-glucosidase
#2: 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.: 2
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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.5M NaCl, 0.1M Bis-Tris propane, 18% PEG 4000, pH 7.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9175 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9175 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 76095 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.181 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
3.2-3.314.10.576100
3.31-3.454.10.4299.9
3.45-3.64.10.327100
3.6-3.794.10.27499.9
3.79-4.034.10.22699.9
4.03-4.344.20.181100
4.34-4.784.20.15299.8
4.78-5.474.30.14299.7
5.47-6.894.30.13299.5
6.89-504.20.08398.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→45.83 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 1 / SU B: 22.772 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3802 5 %RANDOM
Rwork0.22531 ---
obs0.2266 72039 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.195 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27420 0 248 0 27668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02228501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.93638986
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10653476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47724.1861376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.433154125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.10615138
X-RAY DIFFRACTIONr_chiral_restr0.0890.24271
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222265
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.211617
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.219365
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2596
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4131.517666
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.741228044
X-RAY DIFFRACTIONr_scbond_it0.84312457
X-RAY DIFFRACTIONr_scangle_it1.4514.510942
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6710 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
3Ctight positional0.040.05
4Dtight positional0.040.05
1Atight thermal0.070.5
2Btight thermal0.080.5
3Ctight thermal0.060.5
4Dtight thermal0.060.5
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 275 -
Rwork0.307 5216 -
obs--100 %

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