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- PDB-5ny5: The apo structure of 3,4-dihydroxybenzoic acid decarboxylases fro... -

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Basic information

Entry
Database: PDB / ID: 5ny5
TitleThe apo structure of 3,4-dihydroxybenzoic acid decarboxylases from Enterobacter cloacae
Components3,4-dihydroxybenzoate decarboxylase
KeywordsHYDROLASE / UbiD-family / Carboxylation / Catechols / Prenylated FMN
Function / homologyUbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain / carboxy-lyase activity / 3,4-dihydroxybenzoate decarboxylase
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.501 Å
AuthorsDordic, A. / Gruber, K. / Payer, S. / Glueck, S. / Pavkov-Keller, T. / Marshall, S. / Leys, D.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science Fund Austria
FFG Austria
CitationJournal: Angew Chem Int Ed Engl / Year: 2017
Title: Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase.
Authors: Stefan E Payer / Stephen A Marshall / Natalie Bärland / Xiang Sheng / Tamara Reiter / Andela Dordic / Georg Steinkellner / Christiane Wuensch / Susann Kaltwasser / Karl Fisher / Stephen E J ...Authors: Stefan E Payer / Stephen A Marshall / Natalie Bärland / Xiang Sheng / Tamara Reiter / Andela Dordic / Georg Steinkellner / Christiane Wuensch / Susann Kaltwasser / Karl Fisher / Stephen E J Rigby / Peter Macheroux / Janet Vonck / Karl Gruber / Kurt Faber / Fahmi Himo / David Leys / Tea Pavkov-Keller / Silvia M Glueck /
Abstract: The utilization of CO as a carbon source for organic synthesis meets the urgent demand for more sustainability in the production of chemicals. Herein, we report on the enzyme-catalyzed para- ...The utilization of CO as a carbon source for organic synthesis meets the urgent demand for more sustainability in the production of chemicals. Herein, we report on the enzyme-catalyzed para-carboxylation of catechols, employing 3,4-dihydroxybenzoic acid decarboxylases (AroY) that belong to the UbiD enzyme family. Crystal structures and accompanying solution data confirmed that AroY utilizes the recently discovered prenylated FMN (prFMN) cofactor, and requires oxidative maturation to form the catalytically competent prFMN species. This study reports on the in vitro reconstitution and activation of a prFMN-dependent enzyme that is capable of directly carboxylating aromatic catechol substrates under ambient conditions. A reaction mechanism for the reversible decarboxylation involving an intermediate with a single covalent bond between a quinoid adduct and cofactor is proposed, which is distinct from the mechanism of prFMN-associated 1,3-dipolar cycloadditions in related enzymes.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 18, 2020Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence / Item: _pdbx_struct_assembly_auth_evidence.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3,4-dihydroxybenzoate decarboxylase
B: 3,4-dihydroxybenzoate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6026
Polymers108,2342
Non-polymers3684
Water4,234235
1
B: 3,4-dihydroxybenzoate decarboxylase
hetero molecules

B: 3,4-dihydroxybenzoate decarboxylase
hetero molecules

B: 3,4-dihydroxybenzoate decarboxylase
hetero molecules

A: 3,4-dihydroxybenzoate decarboxylase
hetero molecules

A: 3,4-dihydroxybenzoate decarboxylase
hetero molecules

A: 3,4-dihydroxybenzoate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,80718
Polymers324,7026
Non-polymers1,10512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation13_544x+1/3,y-1/3,z-1/31
crystal symmetry operation14_654-y+4/3,x-y+2/3,z-1/31
crystal symmetry operation15_554-x+y+1/3,-x+2/3,z-1/31
Buried area33020 Å2
ΔGint-192 kcal/mol
Surface area98030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.907, 209.907, 162.179
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein 3,4-dihydroxybenzoate decarboxylase


Mass: 54116.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SeMet variant of EcAroY / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: B2DCZ6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.15 M L-Arginine, 0.075 M sodium acetate pH 5.0, 6 % w/v PGA protein concentrations of 5.5 and 14 mg/mL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→48.06 Å / Num. obs: 47197 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Net I/σ(I): 22.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 19.9 % / Rmerge(I) obs: 0.779 / Num. unique obs: 4613 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.501→48.06 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3
RfactorNum. reflection% reflection
Rfree0.2359 2360 5 %
Rwork0.2014 --
obs0.2032 47196 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7422 0 24 235 7681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037643
X-RAY DIFFRACTIONf_angle_d0.5610405
X-RAY DIFFRACTIONf_dihedral_angle_d15.1054633
X-RAY DIFFRACTIONf_chiral_restr0.0461174
X-RAY DIFFRACTIONf_plane_restr0.0041380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5013-2.55240.35491350.32392571X-RAY DIFFRACTION99
2.5524-2.60790.37761370.28692603X-RAY DIFFRACTION100
2.6079-2.66860.33811390.28152632X-RAY DIFFRACTION100
2.6686-2.73530.3081370.26442607X-RAY DIFFRACTION100
2.7353-2.80920.27771380.24262623X-RAY DIFFRACTION100
2.8092-2.89190.27441380.25352622X-RAY DIFFRACTION100
2.8919-2.98520.32371380.25152618X-RAY DIFFRACTION100
2.9852-3.09190.31591390.26812646X-RAY DIFFRACTION100
3.0919-3.21570.28691380.24872618X-RAY DIFFRACTION100
3.2157-3.3620.2721390.232639X-RAY DIFFRACTION100
3.362-3.53920.25391380.21212627X-RAY DIFFRACTION100
3.5392-3.76080.22281390.19982647X-RAY DIFFRACTION100
3.7608-4.05110.22661390.19132644X-RAY DIFFRACTION100
4.0511-4.45850.1961400.1662645X-RAY DIFFRACTION100
4.4585-5.1030.20711400.15822675X-RAY DIFFRACTION100
5.103-6.42690.18851410.17662666X-RAY DIFFRACTION100
6.4269-48.15410.17761450.1632753X-RAY DIFFRACTION100
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)
11.9590.4137-0.67642.29450.11461.28520.07160.1535-0.03640.023-0.0091-0.29940.07760.1706-0.07620.54190.10390.10040.65440.07160.690640.944297.261250.7682
21.87180.23450.56881.3769-0.14581.9827-0.05240.48410.911-0.34050.1863-0.2014-0.5839-0.1112-0.17360.83390.05450.21110.86430.17971.084241.3656115.074143.6557
31.7117-0.3175-0.41140.8770.34081.36930.13710.52960.3955-0.32930.0409-0.3982-0.26250.169-0.16820.7030.08180.16980.71370.14490.831439.9645109.285847.0284
40.6835-0.7179-0.05471.3145-0.05481.23930.03520.1243-0.10020.0340.12650.277-0.0081-0.4504-0.15060.4986-0.00520.07660.7513-0.03950.73658.922566.560224.225
50.3723-0.5010.54951.5287-0.02171.4567-0.1186-0.06470.25240.44390.1569-0.142-0.23380.1621-0.03110.65310.08240.09880.7778-0.06730.760765.243880.795238.6625
61.4078-0.7862-0.47311.20550.65941.3248-0.0117-0.29170.23040.23440.1484-0.0678-0.1955-0.0991-0.11260.5640.02880.05230.6777-0.06240.634865.896178.092534.7874
71.0570.2791-0.11950.8748-0.21960.8637-0.09650.07010.085-0.02420.05220.1249-0.1025-0.1210.03110.42460.0056-0.02610.4928-0.02090.474185.14967.7910.8709
88.11580.23571.14723.09470.51.0871-0.44720.6455-0.0157-0.25740.20160.5213-0.1979-0.26580.3140.61260.0461-0.12010.70.00410.794461.984555.144-5.1277
91.0068-0.64380.33870.8192-0.02181.04350.029-0.0091-0.01830.0545-0.0244-0.12360.06780.1402-0.01270.43810.00590.00970.45370.04750.440318.5344113.48869.4433
102.66040.05390.58272.5658-0.68121.7446-0.1276-0.2243-0.38360.59030.0692-0.51410.01320.73990.05040.69430.0831-0.07210.810.11190.842928.715188.78485.3262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 223 )
3X-RAY DIFFRACTION3chain 'A' and (resid 224 through 343 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 106 )
5X-RAY DIFFRACTION5chain 'B' and (resid 107 through 221 )
6X-RAY DIFFRACTION6chain 'B' and (resid 222 through 330 )
7X-RAY DIFFRACTION7chain 'B' and (resid 331 through 473 )
8X-RAY DIFFRACTION8chain 'B' and (resid 474 through 491 )
9X-RAY DIFFRACTION9chain 'A' and (resid 344 through 473 )
10X-RAY DIFFRACTION10chain 'A' and (resid 474 through 491)

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