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Basic information

Entry
Database: PDB / ID: 7ac8
TitleMolecular basis for the unique allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex.
Components(Imidazole glycerol phosphate synthase subunit ...) x 2
KeywordsLYASE / Enzyme regulation / Allostery / Ensemble model / conformational changes / HisF / HisH / Imidazole Glycerol Phosphate Synthase / LYASE (4.3.2.10)
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / glutaminase activity / L-histidine biosynthetic process / lyase activity / cytoplasm
Similarity search - Function
Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel ...Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like / Aldolase-type TIM barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / Chem-GUO / PHOSPHATE ION / Imidazole glycerol phosphate synthase subunit HisF / Imidazole glycerol phosphate synthase subunit HisH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSung, S. / Wilmanns, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission664726European Union
CitationJournal: Nat Commun / Year: 2021
Title: Molecular basis for the allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex.
Authors: Wurm, J.P. / Sung, S. / Kneuttinger, A.C. / Hupfeld, E. / Sterner, R. / Wilmanns, M. / Sprangers, R.
History
DepositionSep 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Imidazole glycerol phosphate synthase subunit HisF
B: Imidazole glycerol phosphate synthase subunit HisH
C: Imidazole glycerol phosphate synthase subunit HisF
D: Imidazole glycerol phosphate synthase subunit HisH
E: Imidazole glycerol phosphate synthase subunit HisF
F: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,81012
Polymers153,1226
Non-polymers1,6886
Water10,683593
1
A: Imidazole glycerol phosphate synthase subunit HisF
B: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7644
Polymers51,0412
Non-polymers7232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Imidazole glycerol phosphate synthase subunit HisF
D: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2824
Polymers51,0412
Non-polymers2412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Imidazole glycerol phosphate synthase subunit HisF
F: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7644
Polymers51,0412
Non-polymers7232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.835, 92.835, 168.625
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 251)
21(chain C and (resid 1 through 24 or (resid 25...
31(chain E and (resid 1 through 23 or (resid 24...
12(chain B and (resid 1 through 198 or resid 301))
22(chain D and (resid 1 through 198 or resid 301))
32chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLUGLU(chain A and resid 1 through 251)AA1 - 2511 - 251
211METMETGLUGLU(chain C and (resid 1 through 24 or (resid 25...CC1 - 241 - 24
221ASNASNASNASN(chain C and (resid 1 through 24 or (resid 25...CC2525
231METMETGLYGLY(chain C and (resid 1 through 24 or (resid 25...CC1 - 2521 - 252
241METMETGLYGLY(chain C and (resid 1 through 24 or (resid 25...CC1 - 2521 - 252
251METMETGLYGLY(chain C and (resid 1 through 24 or (resid 25...CC1 - 2521 - 252
311METMETPHEPHE(chain E and (resid 1 through 23 or (resid 24...EE1 - 231 - 23
321GLUGLUASNASN(chain E and (resid 1 through 23 or (resid 24...EE24 - 2524 - 25
331METMETGLUGLU(chain E and (resid 1 through 23 or (resid 24...EE1 - 2511 - 251
341METMETGLUGLU(chain E and (resid 1 through 23 or (resid 24...EE1 - 2511 - 251
351METMETGLUGLU(chain E and (resid 1 through 23 or (resid 24...EE1 - 2511 - 251
361METMETGLUGLU(chain E and (resid 1 through 23 or (resid 24...EE1 - 2511 - 251
112GLYGLYGLYGLY(chain B and (resid 1 through 198 or resid 301))BB02
212GLYGLYGLYGLY(chain D and (resid 1 through 198 or resid 301))DD02
312METMETGLNGLNchain FFF - L1 - 3013

NCS ensembles :
ID
1
2

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Components

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Imidazole glycerol phosphate synthase subunit ... , 2 types, 6 molecules ACEBDF

#1: Protein Imidazole glycerol phosphate synthase subunit HisF / IGP synthase cyclase subunit / IGP synthase subunit HisF / ImGP synthase subunit HisF / IGPS subunit HisF


Mass: 27753.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisF, TM_1036 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9X0C6, imidazole glycerol-phosphate synthase
#2: Protein Imidazole glycerol phosphate synthase subunit HisH / IGP synthase glutaminase subunit / IGP synthase subunit HisH / ImGP synthase subunit HisH / IGPS ...IGP synthase glutaminase subunit / IGP synthase subunit HisH / ImGP synthase subunit HisH / IGPS subunit HisH / TmHisH


Mass: 23286.744 Da / Num. of mol.: 3 / Mutation: C84A
Source method: isolated from a genetically manipulated source
Details: The MG residues at the beginning of the protein chain are from a TEV cleavage site.
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: hisH, TM_1038 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9X0C8, imidazole glycerol-phosphate synthase, glutaminase

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Non-polymers , 4 types, 599 molecules

#3: Chemical ChemComp-GUO / [(2R,3S,4R,5R)-5-[4-aminocarbonyl-5-[(E)-[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]amino]methylideneamino]imidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 577.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H25N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H10N2O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
Details: In chain C, PO4 no. 301 and HOH no. 514 are likely to be part of a larger ligand (ProFAR) with enhanced flexibility.
Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer detailsIn chain C, PO4 no. 301 and HOH no. 514 are likely to be part of a larger ligand (ProFAR) with ...In chain C, PO4 no. 301 and HOH no. 514 are likely to be part of a larger ligand (ProFAR) with enhanced flexibility.

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: Pentaerythritol (5/4 PO/OH), sodium thiocyanate, HEPES, L-glutamine, ProFAR

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Data collection

DiffractionMean temperature: 103.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.06→46.1 Å / Num. obs: 100496 / % possible obs: 99.99 % / Redundancy: 10.3 % / Biso Wilson estimate: 40.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08592 / Net I/σ(I): 16.19
Reflection shellResolution: 2.06→2.134 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.052 / Num. unique obs: 10012 / CC1/2: 0.709 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPW

1gpw


Resolution: 2.06→46.07 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 18.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1861 4833 4.81 %
Rwork0.1564 95660 -
obs0.1578 100493 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.38 Å2 / Biso mean: 49.1507 Å2 / Biso min: 22.91 Å2
Refinement stepCycle: final / Resolution: 2.06→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10656 0 79 593 11328
Biso mean--54.7 58.09 -
Num. residues----1359
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2286X-RAY DIFFRACTION11.667TORSIONAL
12C2286X-RAY DIFFRACTION11.667TORSIONAL
13E2286X-RAY DIFFRACTION11.667TORSIONAL
21B1824X-RAY DIFFRACTION11.667TORSIONAL
22D1824X-RAY DIFFRACTION11.667TORSIONAL
23F1824X-RAY DIFFRACTION11.667TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.06-2.080.31431620.247631893351
2.08-2.110.25781900.230731843374
2.11-2.130.24391620.219231243286
2.13-2.160.25912020.211832203422
2.16-2.190.24721820.204431463328
2.19-2.220.22051380.232253363
2.22-2.250.22551740.189730883262
2.25-2.280.24192020.185631813383
2.28-2.320.22821620.182932473409
2.32-2.360.23481700.182431403310
2.36-2.40.24661140.176132133327
2.4-2.440.19251400.169732663406
2.44-2.490.22911580.177331343292
2.49-2.540.22271460.174132233369
2.54-2.60.21151700.170931913361
2.6-2.660.21171600.171132023362
2.66-2.720.20421760.166331563332
2.72-2.80.18031860.162931803366
2.8-2.880.19072200.159531103330
2.88-2.970.19741740.163131623336
2.97-3.080.18711240.171432413365
3.08-3.20.20311240.167632693393
3.2-3.350.22371180.170831993317
3.35-3.520.18011540.158331993353
3.52-3.740.16532000.144531463346
3.74-4.030.17731500.137932233373
4.03-4.440.13261540.120731793333
4.44-5.080.14341470.119832043351
5.08-6.40.16891220.153532123334
6.4-46.070.17551520.15132073359
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)
11.37590.3370.20131.3672-0.26232.0589-0.0462-0.0737-0.08950.0562-0.0215-0.1526-0.0660.1349-0.00010.24670.0029-0.02650.29-0.01490.299542.2346-32.57667.9554
21.75580.3426-0.12321.52990.09761.3090.05420.01410.1808-0.11560.03210.0105-0.1332-0.0372-0.00010.3148-0.02010.02120.2724-0.00990.279145.2917-12.2321-12.8559
31.661-0.2617-0.33772.5860.41982.15870.08720.2383-0.1515-0.2351-0.16870.1809-0.1996-0.33480.00020.4230.0695-0.02660.4232-0.04610.27950.3632-9.06179.3948
41.2681-0.00910.70831.60150.29382.2996-0.003-0.0963-0.03460.17540.0217-0.3786-0.0173-0.0279-0.00030.44480.0254-0.03430.41680.00090.366912.30810.542334.2706
52.2918-0.3752-0.34471.92490.14231.0225-0.06940.2347-0.2933-0.3353-0.02870.17960.0673-0.0683-0.00040.3498-0.0311-0.02760.3425-0.05760.38286.8691-54.2494-7.7715
61.8215-0.5036-0.38881.29760.12761.353-0.1713-0.3056-0.24530.11110.12860.6331-0.0318-0.2018-0.00170.31510.03230.06450.40890.03520.6472-13.8364-46.958.8715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain C and resseq 1:301)C1 - 301
2X-RAY DIFFRACTION2(chain D and resseq -1:301)D-1 - 301
3X-RAY DIFFRACTION3(chain A and resseq 1:301)A1 - 301
4X-RAY DIFFRACTION4(chain B and resseq -1:301)B-1 - 301
5X-RAY DIFFRACTION5(chain E and resseq 1:301)E1 - 301
6X-RAY DIFFRACTION6(chain F and resseq 1:301)F1 - 301

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