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- PDB-7tbu: Crystal structure of the 5-enolpyruvate-shikimate-3-phosphate syn... -

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Entry
Database: PDB / ID: 7tbu
TitleCrystal structure of the 5-enolpyruvate-shikimate-3-phosphate synthase (EPSPS) domain of Aro1 from Candida albicans in complex with shikimate-3-phosphate
Components5-enolpyruvylshikimate-3-phosphate synthase
KeywordsTRANSFERASE / CHORISMATE BIOSYNTHESIS / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID
Function / homologySHIKIMATE-3-PHOSPHATE
Function and homology information
Biological speciesCandida albicans Ca6 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStogios, P.J. / Evdokimova, E. / Michalska, K. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / 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
DepositionDec 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 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: 5-enolpyruvylshikimate-3-phosphate synthase
B: 5-enolpyruvylshikimate-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2876
Polymers97,5352
Non-polymers7534
Water14,160786
1
A: 5-enolpyruvylshikimate-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1443
Polymers48,7671
Non-polymers3762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5-enolpyruvylshikimate-3-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1443
Polymers48,7671
Non-polymers3762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.987, 159.754, 55.874
Angle α, β, γ (deg.)90.000, 92.275, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 5-enolpyruvylshikimate-3-phosphate synthase


Mass: 48767.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans Ca6 (yeast) / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-S3P / SHIKIMATE-3-PHOSPHATE


Mass: 254.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.4 M NaCl, 0.1 M Tris pH 8, 26%PEG3350 1mM 3-P-Shikimate cryoprotectant: 22%Et.Glycol, HEPES pH7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 66832 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 26.17 Å2 / CC1/2: 0.502 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.041 / Net I/σ(I): 18.1
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 3323 / CC1/2: 0.502 / Rpim(I) all: 0.589 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NVS

3nvs


Resolution: 1.85→29.66 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.7136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1939 3 %RANDOM
Rwork0.1801 62784 --
obs0.1816 64723 96.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.69 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6591 0 48 786 7425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076774
X-RAY DIFFRACTIONf_angle_d0.9759206
X-RAY DIFFRACTIONf_chiral_restr0.06251094
X-RAY DIFFRACTIONf_plane_restr0.00711174
X-RAY DIFFRACTIONf_dihedral_angle_d20.41962520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.31591160.27554098X-RAY DIFFRACTION89.28
1.9-1.950.29061350.26634255X-RAY DIFFRACTION91.46
1.95-2.010.31371310.24564347X-RAY DIFFRACTION94.13
2.01-2.070.27551310.22354422X-RAY DIFFRACTION94.97
2.07-2.140.26731400.21134481X-RAY DIFFRACTION96.94
2.14-2.230.2641350.19994463X-RAY DIFFRACTION97.33
2.23-2.330.2561430.20054518X-RAY DIFFRACTION97.8
2.33-2.450.24621440.19014521X-RAY DIFFRACTION97.76
2.45-2.610.28511480.18924580X-RAY DIFFRACTION98.36
2.61-2.810.23381380.17834577X-RAY DIFFRACTION98.52
2.81-3.090.20971470.17854558X-RAY DIFFRACTION99.14
3.09-3.540.23071400.16344640X-RAY DIFFRACTION99.81
3.54-4.450.18271480.13864645X-RAY DIFFRACTION99.96
4.46-29.660.20081430.17244679X-RAY DIFFRACTION99.63
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)
12.071721960950.760825296928-2.32205625742.12335213884-2.178080308065.3895897353-0.117206033768-0.1766379701480.005232304458620.4727011654230.1120327345620.254113278924-0.0870229622442-0.3229309499320.03491842428580.3024307318970.05283949422880.06191146660370.205116018472-0.008211479960070.22679224421210.754892763273.571437084116.7438162228
22.612941628830.5003159861380.5920448480261.93794090772-0.105772358632.39675558055-0.0475694672812-0.265218007660.03990726896780.0728053330671-0.01061624042220.02248649402940.0346071835450.1343134842020.04464069235870.1164644056510.03246369780420.009463575784050.1645912386390.03934320442520.15133580526830.936727353682.26751757480.0909610914419
33.14647173677-0.45495173511-1.105070378312.41920416490.5315544683373.30141875574-0.04436196652960.0260804621604-0.280962580477-0.1076230880990.0684001065210.3739566131820.457190291495-0.230985290077-0.01161453641590.184891076395-0.0235086424481-0.0505088825320.1126744492810.01923479218470.21683603511220.579240949971.1969861244-6.63888546108
42.02082833344-0.9920249528840.4463858266074.98969249616-1.527524094534.234703120930.0264832769890.125847340591-0.0338675640957-0.7372938056220.1088411948710.5402489658490.201062956615-0.34632035466-0.1291637078310.324166033109-0.0462491972755-0.06835265326510.1901899381010.0320760250520.2364903815915.5893846591460.491888597412.5227146687
55.412668819610.1988826993980.3472446444016.338078051881.473287114167.62474287422-0.0965708035482-0.4423034065050.2707326623070.3789666153450.110112494813-0.785405558742-0.2158711975480.490631397225-0.03758154905570.2885627742720.0216869193284-0.08183433910680.2427595664250.04343073029780.31864175457916.975293041256.765841937624.9667408091
66.28658930133-2.007753355483.410201197938.50888970399-2.077888981532.35941228214-0.308923673635-0.6630096603121.067612588670.7457564701150.09978495321270.147569457308-1.29935181952-0.295059600230.183406522470.7162150470290.05537814395860.009175924458070.545911105257-0.0973837978360.4163636661139.2675358747970.905884071528.8697143995
72.53960323993-0.5716568649661.83903275092.47030520611-0.8477704159283.61219965465-0.04274921206690.501106462534-0.32312454978-0.5925892732710.1807134071460.1074951994240.03500991225810.00818404334247-0.1209473286630.258071804534-0.0973077631261-0.008063796900060.289906712488-0.01612557601090.2113643180597.9050113072100.83608571515.654297143
82.57061849521-0.040109193623-0.8653257348842.8924888003-0.358990775072.59835387468-0.009237021055040.115344778169-0.11354074738-0.150357933973-0.0108106061816-0.1785037367060.1209966186660.1022815558040.02454198751980.118859033282-0.0246193296109-0.01373355874780.1571927275320.0125273118920.15471115094627.045335284397.852025650927.4627179485
91.27518345752-0.223433557831.041904605181.44479056603-0.7994757944862.26434231758-0.0919036634103-0.1295735015530.145286842057-0.01239062093390.128559085270.273528867597-0.349740982396-0.304251933783-0.04718001911430.1930197670160.0397321060580.02793122187890.1773917754050.01212541652220.220565330845.64124755913114.44090032322.8630098834
104.913807725871.90761414339-0.09876227923713.30094824261.202265879947.21242550826-0.1637755009750.23565660427-0.206035051632-0.689078097640.120219608934-0.678107418154-0.07294429680560.429728883153-0.006457132253720.439532616548-0.02544963701850.01414191515810.1595878921170.0001698254142240.29546478473612.8235655182124.9360832596.71422809073
113.922591792580.334709870203-2.401262370753.87580564403-1.058599307697.48097120995-0.1268850838970.550121051238-0.589725756396-1.372728603960.28523100910.1206664941280.4316995175770.349840491438-0.0994556825570.81449646448-0.0745742442862-0.1240856424380.499324488049-0.1278136474620.4757881435453.97538514066110.928195210.115876132021
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 387 through 422 )AA387 - 4221 - 36
22chain 'A' and (resid 423 through 593 )AA423 - 59337 - 207
33chain 'A' and (resid 594 through 639 )AA594 - 639208 - 253
44chain 'A' and (resid 640 through 714 )AA640 - 714254 - 328
55chain 'A' and (resid 715 through 808 )AA715 - 808329 - 422
66chain 'A' and (resid 809 through 841 )AA809 - 841423 - 450
77chain 'B' and (resid 388 through 447 )BC388 - 4471 - 60
88chain 'B' and (resid 448 through 593 )BC448 - 59361 - 206
99chain 'B' and (resid 594 through 710 )BC594 - 710207 - 323
1010chain 'B' and (resid 711 through 795 )BC711 - 795324 - 397
1111chain 'B' and (resid 796 through 841 )BC796 - 841398 - 435

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