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- PDB-3fed: The high resolution structure of human glutamate carboxypeptidase... -

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Basic information

Entry
Database: PDB / ID: 3fed
TitleThe high resolution structure of human glutamate carboxypeptidase III (GCPIII/NAALADase II) in complex with a transition state analog of Glu-Glu
ComponentsGlutamate carboxypeptidase III
KeywordsHYDROLASE / metallopeptidase / bimetallic active site / N-glycosylation / calcium cation / chloride anion / zinc ions / Carboxypeptidase / Dipeptidase / Glycoprotein / Membrane / Metal-binding / Metalloprotease / Multifunctional enzyme / Protease / Signal-anchor / Transmembrane
Function / homology
Function and homology information


carboxylic acid catabolic process / N-formylglutamate deformylase activity / glutamate carboxypeptidase II / Aspartate and asparagine metabolism / dipeptidase activity / dipeptidyl-peptidase activity / carboxypeptidase activity / metallocarboxypeptidase activity / serine-type peptidase activity / proteolysis ...carboxylic acid catabolic process / N-formylglutamate deformylase activity / glutamate carboxypeptidase II / Aspartate and asparagine metabolism / dipeptidase activity / dipeptidyl-peptidase activity / carboxypeptidase activity / metallocarboxypeptidase activity / serine-type peptidase activity / proteolysis / metal ion binding / membrane / plasma membrane
Similarity search - Function
Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A ...Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(bba) Sandwich / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BIX / N-acetylated-alpha-linked acidic dipeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.29 Å
AuthorsLubkowski, J. / Barinka, C. / Hlouchova, K.
CitationJournal: Febs J. / Year: 2009
Title: Structural insight into the evolutionary and pharmacologic homology of glutamate carboxypeptidases II and III
Authors: Hlouchova, K. / Barinka, C. / Konvalinka, J. / Lubkowski, J.
History
DepositionNov 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_conn_angle / pdbx_struct_special_symmetry / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 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: Glutamate carboxypeptidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,54610
Polymers79,9411
Non-polymers1,6069
Water15,511861
1
A: Glutamate carboxypeptidase III
hetero molecules

A: Glutamate carboxypeptidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,09220
Polymers159,8812
Non-polymers3,21118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7570 Å2
ΔGint-99 kcal/mol
Surface area49150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.731, 104.086, 77.634
Angle α, β, γ (deg.)90.00, 108.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-7-

HOH

21A-1054-

HOH

31A-1434-

HOH

41A-1513-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate carboxypeptidase III / GCPIII / N-acetylated-alpha-linked acidic dipeptidase 2 / N-acetylated-alpha-linked acidic ...GCPIII / N-acetylated-alpha-linked acidic dipeptidase 2 / N-acetylated-alpha-linked acidic dipeptidase II / NAALADase II


Mass: 79940.578 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAALAD2 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider's S2 cells / References: UniProt: Q9Y3Q0, glutamate carboxypeptidase II

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Sugars , 2 types, 4 molecules

#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.: 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
#3: 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

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Non-polymers , 5 types, 866 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-BIX / (2S)-2-{[(S)-[(3S)-3-amino-3-carboxypropyl](hydroxy)phosphoryl]methyl}pentanedioic acid


Mass: 311.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO8P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na, 10% (w/v) PEG6000, 5% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→30 Å / Num. all: 227958 / Num. obs: 227958 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.29→1.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 1.9 / Num. unique all: 18560 / % possible all: 79.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
Cootmodel building
REFMAC5.4.0057refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2OR4

2or4


Resolution: 1.29→25 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.954 / SU ML: 0.019 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.14727 2292 1 %RANDOM
Rwork0.13087 ---
obs0.13104 225644 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.382 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.25 Å2
2--0.35 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.29→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5504 0 94 861 6459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226093
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9818293
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74124.043282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.484151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7771536
X-RAY DIFFRACTIONr_chiral_restr0.1250.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214612
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8621.53592
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.70125880
X-RAY DIFFRACTIONr_scbond_it3.56832501
X-RAY DIFFRACTIONr_scangle_it5.1864.52392
X-RAY DIFFRACTIONr_rigid_bond_restr2.05836093
X-RAY DIFFRACTIONr_sphericity_free9.963865
X-RAY DIFFRACTIONr_sphericity_bonded5.47435919
LS refinement shellResolution: 1.29→1.325 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 151 -
Rwork0.22 14444 -
obs--86.01 %
Refinement TLS params.Method: refined / Origin x: 19.354 Å / Origin y: 45.788 Å / Origin z: 13.39 Å
111213212223313233
T-0.0205 Å20.0054 Å2-0.0006 Å2--0.0083 Å2-0.0135 Å2---0.0085 Å2
L0.1285 °2-0.07 °20.0387 °2-0.2001 °2-0.1258 °2--0.2067 °2
S-0.0112 Å °-0.0213 Å °0.0134 Å °0.0151 Å °0.01 Å °-0.0218 Å °-0.0035 Å °0.0497 Å °0.0012 Å °

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