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- PDB-6rv9: Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor i... -

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Basic information

Entry
Database: PDB / ID: 6rv9
TitleCrystal Structure of Glucuronoyl Esterase from Cerrena unicolor inactive S270A variant in complex with the aldouronic acid XUXXR
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 / cellulose binding / carboxylic ester hydrolase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / Glucuronyl esterase, fungi / 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 ...: / Glucuronyl esterase, fungi / 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: 1.64 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 31, 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_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_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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
Revision 2.2Nov 13, 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: 4-O-methyl-glucuronoyl methylesterase
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6656
Polymers86,4222
Non-polymers1,2434
Water9,494527
1
A: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4943
Polymers43,2111
Non-polymers2832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1713
Polymers43,2111
Non-polymers9602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.481, 84.481, 261.732
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-838-

HOH

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Components

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


Mass: 43210.930 Da / Num. of mol.: 2 / 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
#2: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)- ...4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-Xylitol


Type: oligosaccharide / Mass: 738.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,5,4/[h212h][a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-2-2-3-2/a4-b1_b4-c1_c2-d1_c4-e1WURCSPDB2Glycan 1.1.0
[][<C5O4>]{[(1+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}[(4+1)][b-D-Xylp]{}}}}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.: 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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M phosphate-citrate pH 4.2, 0.2 M KCl, 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.64→49.29 Å / Num. obs: 116474 / % possible obs: 99.7 % / Redundancy: 8 % / Biso Wilson estimate: 23.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.028 / Rrim(I) all: 0.079 / Net I/σ(I): 14.1 / Num. measured all: 928607 / Scaling rejects: 22
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
1.64-1.6770.953975156440.6030.3771.0251.899.3
8.98-49.297.30.0361578450.9990.0120.03247.998.1

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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: 1.64→44.497 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.52
RfactorNum. reflection% reflection
Rfree0.2098 5754 4.95 %
Rwork0.1858 --
obs0.187 116315 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.95 Å2 / Biso mean: 31.3122 Å2 / Biso min: 15.78 Å2
Refinement stepCycle: final / Resolution: 1.64→44.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5722 0 133 527 6382
Biso mean--35.51 33.18 -
Num. residues----760
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 (%)
1.64-1.65860.31541790.29993642382199
1.6586-1.67820.32181720.29553591376399
1.6782-1.69860.3092090.276436343843100
1.6986-1.72010.30351710.261136553826100
1.7201-1.74280.2831950.254436473842100
1.7428-1.76660.25951850.249836463831100
1.7666-1.79190.26721840.239936623846100
1.7919-1.81860.26781860.226136383824100
1.8186-1.8470.25871970.224136583855100
1.847-1.87730.241600.221837213881100
1.8773-1.90970.24381980.212236163814100
1.9097-1.94440.23712070.208536203827100
1.9444-1.98180.23141970.204836663863100
1.9818-2.02230.22661910.199636763867100
2.0223-2.06620.22982100.203536423852100
2.0662-2.11430.21761950.193436893884100
2.1143-2.16720.23161820.193937003882100
2.1672-2.22580.22371950.192836623857100
2.2258-2.29130.20331870.190236823869100
2.2913-2.36520.21371950.190136553850100
2.3652-2.44970.2041870.186837053892100
2.4497-2.54780.21871980.18837213919100
2.5478-2.66380.20821880.191536803868100
2.6638-2.80420.23921950.190237053900100
2.8042-2.97980.211850.193709389499
2.9798-3.20980.20112250.19233659388499
3.2098-3.53270.20481860.17763750393699
3.5327-4.04370.17841780.15453750392898
4.0437-5.09340.1642070.14113755396298
5.0934-44.51320.17932100.16684025423599
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)
14.31170.6427-3.32854.3723-0.27176.0320.1335-0.29260.14010.1312-0.0721-0.0231-0.45180.0217-0.07610.3828-0.0097-0.02580.2157-0.01840.152827.43217.897627.6269
23.0573-0.99780.42551.1688-0.2810.36450.0031-0.2162-0.19060.31040.01790.1712-0.0544-0.0289-0.02740.37540.00420.08640.1546-0.02270.172813.07765.720227.7789
30.39750.03190.18891.08870.00110.22240.02730.0305-0.07590.1821-0.05520.27180.0142-0.04780.04360.33550.01610.08120.1565-0.02720.2043.72445.374214.9236
40.78780.06560.05870.7625-0.25230.60760.05090.0963-0.13890.0564-0.0834-0.00040.03760.04480.02050.30880.02990.0450.1578-0.03510.166717.2938-1.745312.8197
50.98690.60870.2170.8268-0.27980.40030.08040.0501-0.20930.0898-0.04860.00850.130.07440.01070.36040.04570.04580.1789-0.02320.257522.6556-10.49815.8817
62.79060.1546-1.49311.7139-0.0393.73340.0846-0.40150.4040.3293-0.02140.0629-0.23890.1728-0.06080.3929-0.03090.02790.2221-0.0580.2394.2113-34.172931.353
71.7526-0.11780.19311.28480.03930.56660.0516-0.21240.14940.3621-0.09730.5495-0.0211-0.2311-0.01690.3897-0.0250.17420.2367-0.0980.4139-11.4142-34.443530.7828
81.5903-1.196-0.77520.96490.8310.97460.2208-0.30590.36120.1877-0.2870.88680.1496-0.65170.72110.21490.09780.27510.3743-0.39831.4105-30.1654-37.204719.5179
90.99410.39770.25251.24270.06940.9902-0.0628-0.01740.14580.3412-0.15620.785-0.0217-0.23010.02770.30020.01730.14470.2232-0.10440.5529-14.7652-34.969218.1204
100.63570.22180.30091.39040.41070.91230.0631-0.0523-0.03480.344-0.18470.42030.1951-0.08430.08760.3063-0.02280.11220.1836-0.05410.2637-6.3224-47.119619.6316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 79 through 98 )A79 - 98
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 147 )A99 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 317 )A148 - 317
4X-RAY DIFFRACTION4chain 'A' and (resid 318 through 422 )A318 - 422
5X-RAY DIFFRACTION5chain 'A' and (resid 423 through 458 )A423 - 458
6X-RAY DIFFRACTION6chain 'B' and (resid 79 through 98 )B79 - 98
7X-RAY DIFFRACTION7chain 'B' and (resid 99 through 149 )B99 - 149
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 205 )B150 - 205
9X-RAY DIFFRACTION9chain 'B' and (resid 206 through 317 )B206 - 317
10X-RAY DIFFRACTION10chain 'B' and (resid 318 through 458 )B318 - 458

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