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- PDB-6c5c: Crystal structure of the 3-dehydroquinate synthase (DHQS) domain ... -

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Basic information

Entry
Database: PDB / ID: 6c5c
TitleCrystal structure of the 3-dehydroquinate synthase (DHQS) domain of Aro1 from Candida albicans SC5314 in complex with NADH
Components3-dehydroquinate synthase
KeywordsLYASE / chorismate biosynthesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / phosphorylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / 3-dehydroquinate synthase AroB / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate kinase/Threonine synthase-like 1 ...Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / 3-dehydroquinate synthase AroB / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / Shikimate dehydrogenase substrate binding, N-terminal / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / Shikimate dehydrogenase substrate binding domain / EPSP synthase signature 2. / Rossmann fold - #1970 / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Aminoacid dehydrogenase-like, N-terminal domain superfamily / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pentafunctional AROM polypeptide
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMichalska, K. / Evdokimova, E. / Di Leo, R. / Stogios, P.J. / Savchenko, A. / Joachimiak, A. / Satchell, K. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Life Sci Alliance / Year: 2022
Title: Molecular analysis and essentiality of Aro1 shikimate biosynthesis multi-enzyme in .
Authors: Peter J Stogios / Sean D Liston / Cameron Semper / Bradley Quade / Karolina Michalska / Elena Evdokimova / Shane Ram / Zbyszek Otwinowski / Dominika Borek / Leah E Cowen / Alexei Savchenko /
Abstract: In the human fungal pathogen , encodes an essential multi-enzyme that catalyses consecutive steps in the shikimate pathway for biosynthesis of chorismate, a precursor to folate and the aromatic ...In the human fungal pathogen , encodes an essential multi-enzyme that catalyses consecutive steps in the shikimate pathway for biosynthesis of chorismate, a precursor to folate and the aromatic amino acids. We obtained the first molecular image of Aro1 that reveals the architecture of all five enzymatic domains and their arrangement in the context of the full-length protein. Aro1 forms a flexible dimer allowing relative autonomy of enzymatic function of the individual domains. Our activity and in cellulo data suggest that only four of Aro1's enzymatic domains are functional and essential for viability of , whereas the 3-dehydroquinate dehydratase (DHQase) domain is inactive because of active site substitutions. We further demonstrate that in , the type II DHQase Dqd1 can compensate for the inactive DHQase domain of Aro1, suggesting an unrecognized essential role for this enzyme in shikimate biosynthesis. In contrast, in and , which do not encode a Dqd1 homolog, Aro1 DHQase domains are enzymatically active, highlighting diversity across species.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 14, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Nov 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinate synthase
B: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,73818
Polymers85,5692
Non-polymers2,16916
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint1 kcal/mol
Surface area31180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.678, 92.060, 88.915
Angle α, β, γ (deg.)90.00, 97.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-dehydroquinate synthase / / Aro1p


Mass: 42784.645 Da / Num. of mol.: 2 / Fragment: UNP residues 1-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ARO1, CAALFM_C400890WA, CaO19.12175, CaO19.4704 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Gold / References: UniProt: Q5AME2, 3-dehydroquinate synthase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium thiocyanate, 20% PEG3350, 2 mM NADH, 0.5 mM zinc chloride, cryoprotectant: 8% glycerol, 8% ethylene glycol, 8% sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 5, 2017 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 69649 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 37.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 3533 / CC1/2: 0.717 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
SBC-Collectdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SG6

1sg6


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 6.857 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2108 3.1 %RANDOM
Rwork0.17606 ---
obs0.17695 66446 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.338 Å2
Baniso -1Baniso -2Baniso -3
1-3 Å20 Å21.23 Å2
2---1.3 Å20 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 141 389 6438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196178
X-RAY DIFFRACTIONr_bond_other_d0.0020.026051
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9958340
X-RAY DIFFRACTIONr_angle_other_deg0.99314024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7025771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44124.249233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6111534
X-RAY DIFFRACTIONr_chiral_restr0.0940.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026647
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021173
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_it0.6021.5513087
X-RAY DIFFRACTIONr_mcbond_other0.6011.5513086
X-RAY DIFFRACTIONr_mcangle_it0.9392.3213857
X-RAY DIFFRACTIONr_mcangle_other0.9392.3213858
X-RAY DIFFRACTIONr_scbond_it0.9311.7523091
X-RAY DIFFRACTIONr_scbond_other0.9291.7523091
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3742.5624484
X-RAY DIFFRACTIONr_long_range_B_refined5.39220.0376922
X-RAY DIFFRACTIONr_long_range_B_other5.39220.0456923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 139 -
Rwork0.307 4880 -
obs--99.01 %
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)
12.36850.12360.21722.58520.80433.03860.10020.01630.00060.0275-0.07830.4722-0.1136-0.3636-0.02190.0275-0.0026-0.03860.25110.01490.2573-26.2409-10.2767-12.7413
23.793-0.5188-0.24642.0167-0.0372.3514-0.0678-0.17620.26970.23420.00940.2342-0.2706-0.21450.05850.1395-0.032-0.01590.2068-0.01590.2209-17.3787-3.3605-2.8882
31.9755-0.1921.78212.0456-0.36063.20560.0570.0617-0.04630.0335-0.0714-0.0202-0.050.0930.01440.0189-0.0336-0.0330.17020.01420.1532-11.8393-13.3925-9.8895
41.4416-0.7161-1.41973.21321.96342.31210.0370.33930.0132-0.7039-0.15250.1596-0.2018-0.2940.11560.25170.0101-0.09720.29510.02640.1858-17.9649-15.1499-31.8695
54.0844-1.42351.10767.3292-3.92786.41890.04010.0879-0.0302-0.56850.12290.7195-0.1423-0.5476-0.1630.15310.0038-0.09010.3177-0.07640.2273-23.7105-16.0567-27.367
66.0872.8476-5.53342.5985-5.291210.8560.0291-0.522-1.3113-0.3949-0.2102-0.1411.02720.4310.18120.72760.0229-0.11180.42110.08280.5803-12.9935-33.1284-15.2924
72.3025-0.22270.21562.52030.04082.1527-0.01690.1973-0.0301-0.35330.0053-0.27310.06460.17890.01160.24860.01060.02770.28160.01310.1793-3.8224-22.681-33.432
86.6525-2.15742.08958.81170.8057.31050.0050.32920.9633-0.4262-0.1286-0.5718-0.39360.54220.12360.4742-0.09570.0850.41630.10290.40094.6832-9.435-35.9883
94.5070.0172-1.12056.8456-0.462311.999-0.0853-0.2938-0.39530.1160.0723-0.25410.40830.13550.0130.21740.0237-0.00610.4230.00110.40718.31-24.9874-22.4892
104.7099-1.0976-0.3442.20780.17073.0027-0.15630.0689-0.329-0.11690.0793-0.35640.26210.29010.07690.38580.05990.04010.2707-0.00280.3116-1.4421-33.697-30.2106
115.6491-1.60813.08982.7702-1.23224.70470.0147-0.0837-0.00280.1220.0309-0.01650.06880.0692-0.04560.2735-0.01870.0280.2384-0.01960.29581.5828-38.123717.4724
120.8957-1.03080.32861.9183-0.92644.5388-0.13370.03920.04570.2272-0.1466-0.29120.29730.64990.28030.07720.0197-0.05850.29840.06610.23710.7028-29.95869.4965
130.89290.00670.07164.19140.57485.1235-0.1221-0.03290.10550.2402-0.1075-0.58380.01741.07680.22970.0457-0.0407-0.10850.56740.14520.37817.3097-25.52686.0593
142.12-1.0399-1.38893.274-0.28733.7301-0.04750.10620.11890.1055-0.1533-0.2367-0.33930.42170.20080.0759-0.0998-0.09580.26790.06240.1986.5737-15.728-0.8871
151.3264-0.35690.94512.4758-2.09594.1499-0.1462-0.00090.10750.3843-0.0339-0.0785-0.32810.0420.18010.0913-0.0425-0.06770.18360.01050.15310.5968-19.77168.7967
163.3492-0.1685-1.57041.2972-0.41972.8266-0.0115-0.45490.08310.5783-0.0664-0.1928-0.19420.53390.07790.3805-0.033-0.13160.3130.00250.17764.5433-23.541531.0407
179.3518-0.96363.86923.6997-0.17445.64060.0007-0.1367-0.43670.177-0.0137-0.08410.1160.1010.0130.30920.02260.01860.18710.00820.17231.1648-31.048824.949
180.70111.8871.26675.30654.32277.782-0.14680.01730.0982-0.41020.00560.41760.31-0.0440.14130.47530.0054-0.03780.5065-0.04240.5592-17.91-31.391315.3932
192.74060.8131-0.75612.3579-0.22882.204-0.0489-0.10520.26870.13190.04740.0641-0.2418-0.06840.00150.38640.014-0.040.2376-0.03110.1762-10.238-15.383231.7487
203.76142.5188-0.82756.09650.28731.2050.06350.11340.6825-0.0084-0.04730.6992-0.391-0.2669-0.01610.46420.0297-0.00650.37370.00150.2792-14.9731-9.948529.6674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 56
2X-RAY DIFFRACTION2A57 - 105
3X-RAY DIFFRACTION3A106 - 171
4X-RAY DIFFRACTION4A172 - 221
5X-RAY DIFFRACTION5A222 - 246
6X-RAY DIFFRACTION6A247 - 257
7X-RAY DIFFRACTION7A258 - 324
8X-RAY DIFFRACTION8A325 - 339
9X-RAY DIFFRACTION9A340 - 359
10X-RAY DIFFRACTION10A360 - 387
11X-RAY DIFFRACTION11B-2 - 11
12X-RAY DIFFRACTION12B12 - 46
13X-RAY DIFFRACTION13B47 - 80
14X-RAY DIFFRACTION14B81 - 106
15X-RAY DIFFRACTION15B107 - 172
16X-RAY DIFFRACTION16B173 - 225
17X-RAY DIFFRACTION17B226 - 249
18X-RAY DIFFRACTION18B250 - 256
19X-RAY DIFFRACTION19B257 - 321
20X-RAY DIFFRACTION20B322 - 387

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