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- PDB-6ru1: Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor i... -

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Basic information

Entry
Database: PDB / ID: 6ru1
TitleCrystal Structure of Glucuronoyl Esterase from Cerrena unicolor inactive S270A variant in complex with the aldouronic acid Um4X
Components4-O-methyl-glucuronoyl methylesterase
KeywordsHYDROLASE / CE15 / esterase / alpha/beta-hydrolase / ligand-bound
Function / homology
Function and homology information


(4-O-methyl)-D-glucuronate-lignin esterase / lignin catabolic process / carboxylic ester hydrolase activity / cellulose binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-O-methyl-glucuronoyl methylesterase
Similarity search - Component
Biological speciesCerrena unicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
Model detailsS270A variant in complex with the aldouronic acid Um4X
AuthorsErnst, H.A. / Mosbech, C. / Langkilde, A. / Westh, P. / Meyer, A. / Agger, J.W. / Larsen, S.
CitationJournal: Nat Commun / Year: 2020
Title: The structural basis of fungal glucuronoyl esterase activity on natural substrates.
Authors: Ernst, H.A. / Mosbech, C. / Langkilde, A.E. / Westh, P. / Meyer, A.S. / Agger, J.W. / Larsen, S.
History
DepositionMay 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_special_symmetry / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-O-methyl-glucuronoyl methylesterase
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06614
Polymers86,4222
Non-polymers1,64512
Water13,223734
1
A: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7706
Polymers43,2111
Non-polymers5605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2968
Polymers43,2111
Non-polymers1,0857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.240, 84.240, 260.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-886-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4-O-methyl-glucuronoyl methylesterase / Glucuronoyl esterase / GE


Mass: 43210.930 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: S270A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cerrena unicolor (fungus) / Plasmid: pPICZ-alpha / Production host: Komagataella pastoris (fungus) / Variant (production host): X-33
References: UniProt: A0A0A7EQR3, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 472.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-1-2/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}}}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 / N-Acetylglucosamine


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 , 4 types, 743 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7, 0.1 M KCl, 25% w/v SOKALAN CP7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.39→49.14 Å / Num. obs: 188224 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 12.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.038 / Rrim(I) all: 0.107 / Net I/σ(I): 11 / Num. measured all: 1377160 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.39-1.417.21.0026596391240.6920.3851.0781.898.7
7.61-49.147.10.032916512990.9990.0120.03439.795

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RTV

6rtv


Resolution: 1.39→42.12 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.51
RfactorNum. reflection% reflection
Rfree0.1768 9369 4.98 %
Rwork0.1625 --
obs0.1632 188017 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.37 Å2 / Biso mean: 16.1593 Å2 / Biso min: 8.1 Å2
Refinement stepCycle: final / Resolution: 1.39→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 195 734 6747
Biso mean--28.23 25.64 -
Num. residues----772
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3895-1.40530.25423130.23625830614398
1.4053-1.42180.24413140.22958276141100
1.4218-1.43910.25892950.223959286223100
1.4391-1.45740.22843030.217659246227100
1.4574-1.47650.22573140.207158816195100
1.4765-1.49680.21733050.203159096214100
1.4968-1.51820.21492760.195259096185100
1.5182-1.54080.21323300.192858996229100
1.5408-1.56490.20483300.177458806210100
1.5649-1.59060.193250.170659086233100
1.5906-1.6180.18753000.167659086208100
1.618-1.64740.19293240.168459076231100
1.6474-1.67910.20093020.172859386240100
1.6791-1.71340.18453260.165759246250100
1.7134-1.75060.20922960.168359546250100
1.7506-1.79130.18333030.163359576260100
1.7913-1.83610.15773120.159359596271100
1.8361-1.88580.16722810.155159376218100
1.8858-1.94130.17353320.155959536285100
1.9413-2.00390.17633210.154359886309100
2.0039-2.07560.19593310.156159176248100
2.0756-2.15870.16092990.152860156314100
2.1587-2.25690.16973070.157359656272100
2.2569-2.37590.16643130.157559996312100
2.3759-2.52470.17873230.15865979630299
2.5247-2.71960.1633050.15986059636499
2.7196-2.99320.17343110.16156023633499
2.9932-3.42620.17053320.1596037636999
3.4262-4.3160.15113100.14296065637598
4.316-42.13930.15683360.15146269660596
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)
12.67290.1291-1.4452.27780.8114.94250.0917-0.21990.25050.1756-0.03510.0444-0.2286-0.104-0.0490.11280.0041-0.03520.1167-0.01630.134344.19277.710435.8964
21.6945-0.48340.36990.5526-0.06930.62670.0155-0.0538-0.01860.0587-0.00690.0632-0.0006-0.0625-0.00940.1049-0.00070.01510.0749-0.0150.103726.470610.345427.8826
30.99431.51711.12026.98765.44455.45450.0125-0.00790.0311-0.36020.04610.0225-0.319-0.1027-0.04180.10510.0380.00750.1363-0.00050.167211.946917.08419.2897
41.2087-0.5153-1.18840.8757-0.09173.3358-0.1210.0793-0.12990.01020.01320.17510.2551-0.31770.08790.1157-0.0277-0.00130.1359-0.02390.170912.2043-1.925918.5195
50.5470.019-0.06910.5353-0.0540.36760.0060.03780.0336-0.0059-0.01170.0402-0.0123-0.02260.00450.10890.0037-0.00130.0928-0.00190.101830.94776.823817.1337
61.0710.0964-0.14450.64070.17760.86170.00840.0016-0.09120.0174-0.0210.04740.0683-0.01550.01320.12760.0019-0.00180.07570.00060.119134.0894-10.137720.927
72.55190.2756-0.36932.1122-0.55632.9697-0.0048-0.2560.07280.21060.00070.0471-0.058-0.0685-0.01930.109-0.0039-0.02230.0935-0.02130.0965.455648.095131.2272
80.3702-0.067-0.06320.39820.01580.2572-0.00840.0135-0.01360.01010.00010.07040.0009-0.01730.00850.1290.0045-0.00370.0961-0.00090.111445.361248.535715.3563
93.2658-1.50011.91880.8912-0.35872.8299-0.01370.1120.14670.0175-0.0848-0.0418-0.14550.10020.09790.1322-0.01070.00180.06970.0160.095763.562357.448410.8506
100.38320.2023-0.08190.5728-0.15590.3144-0.00010.0345-0.0481-0.0319-0.01690.00270.0502-0.0020.01680.12320.0108-0.00350.1003-0.00510.11358.451736.275613.5659
110.87440.47360.01530.60480.05940.37920.02-0.0273-0.11150.0155-0.0147-0.03210.03720.06610.0060.13040.0224-0.00280.09320.00990.12264.838731.959515.7687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 73 through 110 )B73 - 110
2X-RAY DIFFRACTION2chain 'B' and (resid 111 through 149 )B111 - 149
3X-RAY DIFFRACTION3chain 'B' and (resid 150 through 172 )B150 - 172
4X-RAY DIFFRACTION4chain 'B' and (resid 173 through 205 )B173 - 205
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 370 )B206 - 370
6X-RAY DIFFRACTION6chain 'B' and (resid 371 through 458 )B371 - 458
7X-RAY DIFFRACTION7chain 'A' and (resid 73 through 128 )A73 - 128
8X-RAY DIFFRACTION8chain 'A' and (resid 129 through 317 )A129 - 317
9X-RAY DIFFRACTION9chain 'A' and (resid 318 through 338 )A318 - 338
10X-RAY DIFFRACTION10chain 'A' and (resid 339 through 422 )A339 - 422
11X-RAY DIFFRACTION11chain 'A' and (resid 423 through 458 )A423 - 458

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