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- PDB-7tbv: Crystal structure of the shikimate kinase + 3-dehydroquinate dehy... -

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Entry
Database: PDB / ID: 7tbv
TitleCrystal structure of the shikimate kinase + 3-dehydroquinate dehydratase + 3-dehydroshikimate dehydrogenase domains of Aro1 from Candida albicans
ComponentsPentafunctional AROM polypeptide
KeywordsTRANSFERASE / OXIDOREDUCTASE / CHORISMATE BIOSYNTHESIS / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID
Biological speciesCandida albicans Ca6 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

Deposited unit
A: Pentafunctional AROM polypeptide
B: Pentafunctional AROM polypeptide
C: Pentafunctional AROM polypeptide
D: Pentafunctional AROM polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,28723
Polymers309,9214
Non-polymers1,36519
Water34,6971926
1
A: Pentafunctional AROM polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9087
Polymers77,4801
Non-polymers4286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentafunctional AROM polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6894
Polymers77,4801
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pentafunctional AROM polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6894
Polymers77,4801
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pentafunctional AROM polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0018
Polymers77,4801
Non-polymers5207
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.682, 89.239, 270.708
Angle α, β, γ (deg.)90.000, 90.283, 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
Pentafunctional AROM polypeptide


Mass: 77480.289 Da / Num. of mol.: 4
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1926 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium formate, 12% PEG3350, 1 mM ATP, 2 mM shikimate-3-phosphate

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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: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 163233 / % possible obs: 99 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.49 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.063 / Net I/σ(I): 13.96
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 8117 / CC1/2: 0.656 / Rpim(I) all: 0.595 / % possible all: 99.5

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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: 5SWV

5swv


Resolution: 2.3→29.82 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.6425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1926 1.22 %RANDOM
Rwork0.178 155591 --
obs0.1786 157517 95.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.93 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21338 0 84 1926 23348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003421838
X-RAY DIFFRACTIONf_angle_d0.548929513
X-RAY DIFFRACTIONf_chiral_restr0.0423308
X-RAY DIFFRACTIONf_plane_restr0.00393777
X-RAY DIFFRACTIONf_dihedral_angle_d21.76228095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.35711230.294710042X-RAY DIFFRACTION86.47
2.35-2.420.29141360.271910651X-RAY DIFFRACTION91.63
2.42-2.490.27621350.251710697X-RAY DIFFRACTION92.38
2.49-2.570.30091300.2310784X-RAY DIFFRACTION92.95
2.57-2.660.23981370.212210779X-RAY DIFFRACTION93.16
2.66-2.770.241330.205710918X-RAY DIFFRACTION93.56
2.77-2.890.24321360.197511219X-RAY DIFFRACTION96.17
2.89-3.040.24491360.193811257X-RAY DIFFRACTION96.91
3.04-3.240.23851430.181511429X-RAY DIFFRACTION97.92
3.24-3.480.22681430.170511316X-RAY DIFFRACTION97.23
3.48-3.830.21471450.152811521X-RAY DIFFRACTION98.68
3.83-4.390.18021450.135611664X-RAY DIFFRACTION99.29
4.39-5.520.16741390.142811511X-RAY DIFFRACTION97.97
5.52-29.820.23151450.169311803X-RAY DIFFRACTION98.54
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)
14.72830496699-1.292763724063.763739222150.42389812196-1.121638175298.58943757285-0.182527694606-0.7832114494360.3216372617030.07728572518970.1173621129170.0451183470098-0.535848259459-0.98398134090.04017605008560.2901194564680.07333416584540.03237340331690.284309962754-0.01515420493960.275591363038-10.8239171506-19.645311287432.8807353466
24.13004569284-1.649555488962.392884409350.895266951669-0.4245856770666.37868701321-0.112133259109-0.2377005026410.165431213735-0.0215262264064-0.0401790610545-0.07987003213440.04009660381240.380667922430.1009995398460.2693225763020.0116751517645-0.01326026157810.2130809504470.01265990708140.206888535668-2.55997177975-24.272991800428.9354462169
31.05384113499-0.371720449713-0.3804462759270.343257325249-0.735770213435.99916732506-0.03469674232330.2040367333550.3135722884540.04288123841430.1174329109940.261659834058-0.0952504602917-0.638497949424-0.01956485612810.1882859435050.04383848870280.0009538073733730.2122182301110.01310080105610.294755563127-14.3402324298-20.51536031427.87933665065
40.969674199016-0.3972574251480.1435345565521.82590101794-0.1226601987251.982570573330.06548361425560.0221189995641-0.08500900517130.125362967409-0.00266239143004-0.1531531633290.2998486670380.0234353442452-0.04537008216410.2386348370450.00113287886175-0.02006077205110.07338042377690.003817362939050.266919931055-2.10660996099-30.7302210435-3.53485233417
51.43015534685-0.323203347127-0.4931264543921.214685787350.7166547632012.132312720460.05544347316640.2693220311260.192965797413-0.148953517746-0.1528588307680.287481768563-0.154143023999-0.6365209246350.07175742124840.206721215970.024716305774-0.02939474256940.2527241586550.02706566265250.324457016689-25.9490051535-11.843438706-10.4574866925
64.296660219170.0123751878803-0.9494960246454.146701421981.028442181753.19179150234-0.164161487015-0.244154798020.1114093197240.1911727192010.1630485271590.190729383069-0.338700137205-0.4935414528960.008147043388360.27144633790.129284094920.02259475196790.3501496186140.0007701696676140.292326563613-34.799477943-4.3309707420219.2682756074
71.26452399293-0.865029423273-1.393468936652.034981734531.609052575626.176384662810.00262864084464-0.1216373605780.402249336880.03929464267180.0882389201932-0.01259945814-0.4748736844870.0144457798753-0.08617713231950.1772939216710.02912434728790.01671639594140.178487586765-0.008399933054960.395356366639-22.3075000655-2.215052502225.24774559592
80.3427015304470.1272783551471.64238218947-0.4465260153920.3635326054718.26760235250.02141853523810.2337358930190.0518717197415-0.0406073732748-0.003920514189830.0129702716973-0.3012417103490.297803404043-0.03030830180610.4122689729680.00284056318943-0.03652369510980.4809751741760.06220286523650.330426414796-17.6255918929-20.3023252994-72.5869607467
92.113755511770.200585334498-0.5448186398981.990415374660.389721095974.231410529330.02420550536580.2959264848640.0586515851511-0.2466448108530.04917026868430.0330515642297-0.0494841321642-0.0359424915306-0.03126138238970.181595164640.0234774014693-0.00828593005560.2445358631540.01554940658690.189446413005-15.1044029112-24.6703150703-42.1282807595
102.29975998003-0.105224948683-2.171136944180.9657221723770.4107893646434.682437235980.223379594841-0.09118738124450.232386128238-0.0710163404640.210706291258-0.16139118914-0.4921405446861.31589248192-0.299423848040.498335285706-0.09642798709150.143744008720.888961260143-0.0827317428940.44712500362313.1427227957-16.3701988767-61.7335099972
110.529597044702-0.3712953075352.02604205106-0.275684194808-1.623244742797.84153000505-0.00830743731876-0.1430777153260.0770715396174-0.06942322091590.03348512976310.0700901626572-0.246353172032-0.363663735537-0.01803448040320.41933894014-0.0472863607746-0.07276036792010.637697940868-0.004568860033110.358097090584-20.849762235120.4705261231-58.7235118348
122.020073165790.0586238544444-2.0653965590.783288881509-0.2790617749764.536964919720.243512933138-0.03237264511590.115036391860.164205169861-0.03044735460660.0698937692645-0.284564031075-0.49708003599-0.1555107210990.360726928391-0.0607279112418-0.03166063508780.38846868886-0.007807099492660.28396394855-35.088848955926.5946034779-82.3859945095
133.51327473758-0.9652669636922.715335658321.08178478962-1.180945973437.03557542244-0.0985450085333-0.4073337295260.183259530016-0.00779372908877-0.01422247501460.00346183807164-0.012474610532-0.109872318440.09262857761830.278759386510.02662669543990.03283145632740.2536379254560.005522486420420.244354869553-43.6961658378-18.0402551474-104.789946187
141.47142947599-0.267672738251-0.004518681160812.034642584590.06464226029072.393738956210.009821538853480.0645031161574-0.09357842091940.0153049411571-0.0210913335542-0.05738612476020.145054231282-0.09290991175240.007996838099870.224321272246-0.0154751539184-0.009744632397290.1124320120810.006336179296590.219047798148-42.1822039424-22.7712873216-138.550621802
151.78954365603-0.616420429738-0.8077751199731.31535331193-0.0287636203983.43491845549-0.0210159576584-0.05318487612810.1723675159030.1270655787560.0474165085340.291022300183-0.299511004827-0.642034452002-0.006277456140290.2445347107070.06694350842220.0145321611910.3278398463910.002289191759960.405218778377-68.9395622356-0.544545644333-130.435633877
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 856 through 909 )AA856 - 9091 - 54
22chain 'A' and (resid 910 through 1013 )AA910 - 101355 - 144
33chain 'A' and (resid 1014 through 1044 )AA1014 - 1044145 - 175
44chain 'A' and (resid 1045 through 1226 )AA1045 - 1226176 - 357
55chain 'A' and (resid 1227 through 1381 )AA1227 - 1381358 - 512
66chain 'A' and (resid 1382 through 1502 )AA1382 - 1502513 - 633
77chain 'A' and (resid 1503 through 1551 )AA1503 - 1551634 - 682
88chain 'B' and (resid 857 through 1095 )BB857 - 10951 - 223
99chain 'B' and (resid 1096 through 1317 )BB1096 - 1317224 - 445
1010chain 'B' and (resid 1318 through 1551 )BB1318 - 1551446 - 679
1111chain 'C' and (resid 857 through 1053 )CC857 - 10531 - 180
1212chain 'C' and (resid 1054 through 1551 )CC1054 - 1551181 - 678
1313chain 'D' and (resid 856 through 1013 )DD856 - 10131 - 142
1414chain 'D' and (resid 1014 through 1255 )DD1014 - 1255143 - 384
1515chain 'D' and (resid 1256 through 1551 )DD1256 - 1551385 - 680

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