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- PDB-6rv7: Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor i... -

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Basic information

Entry
Database: PDB / ID: 6rv7
TitleCrystal Structure of Glucuronoyl Esterase from Cerrena unicolor inactive S270A variant in complex with the aldouronic acid UXXR
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
4beta-beta-xylobiose / 4-O-methyl-glucuronoyl methylesterase
Similarity search - Component
Biological speciesCerrena unicolor (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 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 / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_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 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: 4-O-methyl-glucuronoyl methylesterase
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8157
Polymers86,4222
Non-polymers1,3935
Water9,332518
1
A: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7764
Polymers43,2111
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-O-methyl-glucuronoyl methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0393
Polymers43,2111
Non-polymers8282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.781, 84.781, 260.380
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-835-

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 / 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 , 3 types, 4 molecules

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


Type: oligosaccharide / Mass: 606.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[h212h][a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-2-2-3/a4-b1_b4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][<C5O4>]{[(1+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#4: 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

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Non-polymers , 2 types, 519 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M phosphate-citrate pH 4.2, 0.1 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: 1.73→49.33 Å / Num. obs: 99913 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.049 / Rrim(I) all: 0.129 / Net I/σ(I): 10.3 / Num. measured all: 686893 / Scaling rejects: 39
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
1.73-1.767.11.2763436048300.6250.5121.3771.5100
9.48-49.3360.03943487240.9990.0160.04237.798.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6rtv


Resolution: 1.73→49.327 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.48
RfactorNum. reflection% reflection
Rfree0.194 4947 4.96 %
Rwork0.1656 --
obs0.1669 99779 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.39 Å2 / Biso mean: 23.6803 Å2 / Biso min: 11.63 Å2
Refinement stepCycle: final / Resolution: 1.73→49.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 153 518 6385
Biso mean--33.93 29.34 -
Num. residues----758
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 (%)
1.73-1.74970.27281530.254530553208100
1.7497-1.77030.25081600.243531613321100
1.7703-1.79180.25731610.233530833244100
1.7918-1.81450.25361570.226431283285100
1.8145-1.83840.24971730.216531153288100
1.8384-1.86360.24351340.212331323266100
1.8636-1.89020.23321700.207931163286100
1.8902-1.91840.24081540.207631453299100
1.9184-1.94840.24341800.195430753255100
1.9484-1.98030.22021780.185131243302100
1.9803-2.01450.22881560.179231513307100
2.0145-2.05110.20931780.178930933271100
2.0511-2.09060.24951700.179631343304100
2.0906-2.13330.18941580.165531503308100
2.1333-2.17960.1951540.166931673321100
2.1796-2.23030.17661710.166731393310100
2.2303-2.28610.20931510.175831333284100
2.2861-2.34790.19531730.165631483321100
2.3479-2.4170.19981660.165131313297100
2.417-2.4950.1921660.167331963362100
2.495-2.58420.19541610.161431333294100
2.5842-2.68770.19041630.167131663329100
2.6877-2.810.21341630.170931863349100
2.81-2.95810.19361590.176731813340100
2.9581-3.14340.2091950.17631813376100
3.1434-3.38610.19281610.165832123373100
3.3861-3.72670.17771620.148132173379100
3.7267-4.26570.16321620.13053243340599
4.2657-5.37330.14281780.12473275345399
5.3733-49.34660.16761800.1543462364299
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)
12.7479-0.15040.153.0008-1.00662.76020.0095-0.25460.01080.1991-0.020.0268-0.0596-0.0527-0.01660.2472-0.0266-0.01960.1254-0.03020.125724.0274.244929.2613
20.4018-0.1406-0.00880.87890.04790.3849-0.00520.001-0.05250.1398-0.01510.2255-0.0039-0.05830.01590.2009-0.00480.03860.0978-0.0080.16323.08015.361315.7469
30.48480.0940.01870.4968-0.23970.69530.00450.0584-0.0910.042-0.0341-0.00670.05050.03220.03070.20380.00320.0150.1129-0.01390.16217.1014-2.183712.7199
41.01920.5457-0.14380.9443-0.36290.6252-0.0166-0.0062-0.15650.0651-0.0187-0.02050.08870.07740.05570.23280.03420.01250.1022-0.01060.188922.5253-10.99715.6093
52.4503-0.65760.69181.0229-0.37430.7904-0.059-0.22260.13460.17190.03510.0804-0.141-0.19270.03250.25760.01110.030.1637-0.050.1883-6.8345-35.05731.3994
61.4074-1.3652-0.87561.60661.0153.7309-0.0303-0.00350.1154-0.03250.04960.22260.0043-0.4194-00.17850.0083-0.00050.28940.00210.3477-30.0547-38.110121.2048
71.7812-0.2535-0.29660.8923-0.02960.8852-0.0697-0.00380.06960.09380.03010.2328-0.0909-0.17680.03410.19550.010.01540.1533-0.01230.2161-14.5822-35.828918.84
80.73860.00460.09651.07650.12430.9191-0.0161-0.0161-0.01440.1243-0.01470.15640.0492-0.07490.02210.1674-0.00320.02940.1081-0.01210.1531-6.26-47.742619.9899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 80 through 128 )A80 - 128
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 317 )A129 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 422 )A318 - 422
4X-RAY DIFFRACTION4chain 'A' and (resid 423 through 458 )A423 - 458
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 149 )B80 - 149
6X-RAY DIFFRACTION6chain 'B' and (resid 150 through 205 )B150 - 205
7X-RAY DIFFRACTION7chain 'B' and (resid 206 through 317 )B206 - 317
8X-RAY DIFFRACTION8chain 'B' and (resid 318 through 458 )B318 - 458

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