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- PDB-6hzz: Structure of human D-glucuronyl C5 epimerase -

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Basic information

Entry
Database: PDB / ID: 6hzz
TitleStructure of human D-glucuronyl C5 epimerase
ComponentsD-glucuronyl C5-epimerase
KeywordsISOMERASE / C5-epimerase / heparan sulfate
Function / homology
Function and homology information


heparosan-N-sulfate-glucuronate 5-epimerase / heparosan-N-sulfate-glucuronate 5-epimerase activity / negative regulation of cell projection organization / heparin proteoglycan biosynthetic process / racemase and epimerase activity, acting on carbohydrates and derivatives / HS-GAG biosynthesis / heparan sulfate proteoglycan biosynthetic process / positive regulation of SMAD protein signal transduction / Golgi membrane / positive regulation of cell population proliferation ...heparosan-N-sulfate-glucuronate 5-epimerase / heparosan-N-sulfate-glucuronate 5-epimerase activity / negative regulation of cell projection organization / heparin proteoglycan biosynthetic process / racemase and epimerase activity, acting on carbohydrates and derivatives / HS-GAG biosynthesis / heparan sulfate proteoglycan biosynthetic process / positive regulation of SMAD protein signal transduction / Golgi membrane / positive regulation of cell population proliferation / calcium ion binding / Golgi apparatus / protein homodimerization activity
Similarity search - Function
D-glucuronyl C5-epimerase, C-terminal / D-glucuronyl C5-epimerase / D-glucuronyl C5-epimerase C-terminus / D-glucuronyl C5-epimerase, beta-sandwich domain
Similarity search - Domain/homology
ACETATE ION / D-glucuronyl C5-epimerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsDebarnot, C. / Monneau, Y.R. / Roig-Zamboni, V. / Le Narvor, C. / Goulet, A. / Fadel, F. / Vives, R.R. / Bonnaffe, D. / Lortat-Jacob, H. / Bourne, Y.
Funding support France, 3items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INBS-05 France
French National Research AgencyANR-10-LABX-49-01 France
French National Research AgencyANR-10-LABX-33 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase.
Authors: Debarnot, C. / Monneau, Y.R. / Roig-Zamboni, V. / Delauzun, V. / Le Narvor, C. / Richard, E. / Henault, J. / Goulet, A. / Fadel, F. / Vives, R.R. / Priem, B. / Bonnaffe, D. / Lortat-Jacob, H. / Bourne, Y.
History
DepositionOct 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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_unobs_or_zero_occ_atoms.label_seq_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 2.2Nov 6, 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: D-glucuronyl C5-epimerase
B: D-glucuronyl C5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,80915
Polymers120,6212
Non-polymers4,18913
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-43 kcal/mol
Surface area46150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.820, 99.820, 262.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 102 - 617 / Label seq-ID: 12 - 527

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-glucuronyl C5-epimerase / Heparan sulfate C5-epimerase / Hsepi / Heparin/heparan sulfate:glucuronic acid C5-epimerase / ...Heparan sulfate C5-epimerase / Hsepi / Heparin/heparan sulfate:glucuronic acid C5-epimerase / Heparosan-N-sulfate-glucuronate 5-epimerase


Mass: 60310.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLCE, KIAA0836 / Production host: Homo sapiens (human)
References: UniProt: O94923, heparosan-N-sulfate-glucuronate 5-epimerase

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Sugars , 5 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}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: 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
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-4,6-deoxy-Glcp]{}}}LINUCSPDB-CARE
#6: 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.: 1
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, 379 molecules

#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 21.5% P2K MME, 0.1 M Na cacodylate pH 6.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.52→43.83 Å / Num. obs: 47276 / % possible obs: 99.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 50.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.2
Reflection shellResolution: 2.52→2.67 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PW2

4pw2


Resolution: 2.52→43.83 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 17.509 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2489 5 %RANDOM
Rwork0.176 ---
obs0.178 47276 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.37 Å20 Å2
2---0.73 Å20 Å2
3---2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.52→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8291 0 269 372 8932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0148873
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177848
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.70312062
X-RAY DIFFRACTIONr_angle_other_deg0.9611.67118438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16251046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88522.203454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.727151474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9361548
X-RAY DIFFRACTIONr_chiral_restr0.0750.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021750
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_it2.1723.4334128
X-RAY DIFFRACTIONr_mcbond_other2.1693.4324126
X-RAY DIFFRACTIONr_mcangle_it3.5785.1445159
X-RAY DIFFRACTIONr_mcangle_other3.5785.1445160
X-RAY DIFFRACTIONr_scbond_it2.9254.0654745
X-RAY DIFFRACTIONr_scbond_other2.924.0614738
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8375.9946881
X-RAY DIFFRACTIONr_long_range_B_refined6.67540.5339840
X-RAY DIFFRACTIONr_long_range_B_other6.67540.5189837
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16164 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.52→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 172 -
Rwork0.338 3263 -
obs--93.98 %
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)
10.7742-0.0133-0.23940.87180.12760.6270.00760.0206-0.03330.022-0.01160.0450.0295-0.02910.0040.00530.008-0.00620.03810.00170.097866.3282-83.8888-8.7367
21.5493-0.35630.09651.84730.10821.6155-0.0625-0.1006-0.62290.1169-0.01340.11450.43430.05740.0760.19780.02780.03780.01310.02340.458476.9507-118.5522-4.0601
30.3129-0.19060.00171.04730.3580.40510.03750.07540.0743-0.05080.0113-0.0021-0.12940.0521-0.04880.08640.0090.02990.07290.03430.194766.0487-47.9809-2.8884
42.10730.04760.55323.0411-0.09241.0785-0.19680.57880.7254-0.1337-0.0777-0.343-0.58410.31480.27450.3457-0.1336-0.0480.19620.2570.471172.5927-11.6523-7.8467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A102 - 229
2X-RAY DIFFRACTION1A401 - 617
3X-RAY DIFFRACTION2A230 - 400
4X-RAY DIFFRACTION3B102 - 229
5X-RAY DIFFRACTION3B401 - 617
6X-RAY DIFFRACTION4B230 - 400

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