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- PDB-5v0s: Crystal structure of the ACT domain of prephenate dehydrogenase t... -

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Basic information

Entry
Database: PDB / ID: 5v0s
TitleCrystal structure of the ACT domain of prephenate dehydrogenase tyrA from Bacillus anthracis
ComponentsPrephenate dehydrogenase
KeywordsOXIDOREDUCTASE / prephenate dehydrogenase / tyrA / Bacillus anthracis / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


prephenate dehydrogenase / prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process / NAD+ binding
Similarity search - Function
Prephenate dehydrogenase, dimerization domain / Prephenate dehydrogenase, dimerization domain / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / ACT domain / ACT domain profile. / ACT domain / ACT-like domain ...Prephenate dehydrogenase, dimerization domain / Prephenate dehydrogenase, dimerization domain / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Prephenate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsShabalin, I.G. / Hou, J. / Cymborowski, M.T. / Otwinowski, Z. / Kwon, K. / Christendat, D. / Gritsunov, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118619 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117325 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR029205 United States
CitationJournal: Febs J. / Year: 2020
Title: Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.
Authors: Shabalin, I.G. / Gritsunov, A. / Hou, J. / Slawek, J. / Miks, C.D. / Cooper, D.R. / Minor, W. / Christendat, D.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification ..._pdbx_audit_support.funding_organization / _software.classification / _software.name / _software.version
Revision 1.2Apr 7, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prephenate dehydrogenase
B: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0345
Polymers15,8582
Non-polymers1763
Water1,31573
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-21 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.070, 48.070, 233.395
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A307 - 375
2010B307 - 375

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Components

#1: Protein Prephenate dehydrogenase /


Mass: 7928.929 Da / Num. of mol.: 2 / Fragment: unp residues 307-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: tyrA, GBAA_2954, BASH2_02940 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codonplus-RIL / References: UniProt: Q81P63, prephenate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe full-length protein was subjected to limited proteolysis by chymotrypsin right before ...The full-length protein was subjected to limited proteolysis by chymotrypsin right before crystallization. Only ACT domain is present in the structure

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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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 500 mM NaCl, 5% Glycerol, and 10 mM BME were mixed with 0.2 ul of the MCSG Suite I condition #31 (0.1 M Tris pH=8.5, 0.2 M Calcium chloride, ...Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 500 mM NaCl, 5% Glycerol, and 10 mM BME were mixed with 0.2 ul of the MCSG Suite I condition #31 (0.1 M Tris pH=8.5, 0.2 M Calcium chloride, 25% w/v PEG 4000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 11294 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.018 / Rrim(I) all: 0.057 / Rsym value: 0.053 / Χ2: 1.03 / Net I/av σ(I): 32.5 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
2-2.037.50.6191.74820.8440.1950.6530.6190.63488.1
2.03-2.077.30.4620.9040.150.4890.66992.7
2.07-2.117.50.3320.9590.1090.3520.69195.7
2.11-2.157.40.2630.9880.0870.2790.70996
2.15-2.27.50.2550.9710.0860.2710.7199.1
2.2-2.257.60.2710.9520.0910.2880.72596.5
2.25-2.317.40.2450.9640.0840.2620.7298.1
2.31-2.377.90.1870.9840.0620.1990.70496.4
2.37-2.447.50.1530.9840.0520.1630.79897.7
2.44-2.527.60.1250.9930.0430.1330.78297.9
2.52-2.617.70.1330.9960.0450.1410.80597.1
2.61-2.717.60.0950.9960.0320.1010.83497.6
2.71-2.847.50.0880.9960.030.0940.85298.3
2.84-2.997.40.0720.9970.0250.0770.96397.6
2.99-3.177.50.0530.9980.0180.0561.0398.6
3.17-3.427.30.0420.9980.0150.0451.12799.3
3.42-3.767.40.03810.0130.0411.61499.5
3.76-4.317.20.03410.0120.0361.70798.9
4.31-5.4370.0360.9990.0120.0381.83398.9
5.43-506.40.0370.9990.0140.042.45593.6

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data reduction
HKL-2000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
HKL-3000phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.01→41.63 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.848 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1527 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.157
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 565 5 %RANDOM
Rwork0.1708 ---
obs0.1737 10640 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 226.58 Å2 / Biso mean: 53.642 Å2 / Biso min: 26.68 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.5 Å20 Å2
2--1 Å2-0 Å2
3----3.24 Å2
Refinement stepCycle: final / Resolution: 2.01→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 7 73 1140
Biso mean--75.29 62.51 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191081
X-RAY DIFFRACTIONr_bond_other_d0.0020.021070
X-RAY DIFFRACTIONr_angle_refined_deg1.5012.0041448
X-RAY DIFFRACTIONr_angle_other_deg0.87632430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2635136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54924.18643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55415195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.11157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02202
Refine LS restraints NCS

Ens-ID: 1 / Number: 3876 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.007→2.059 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 33 -
Rwork0.262 657 -
all-690 -
obs--85.61 %
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)
112.33977.5603-9.449518.6227-14.01522.3098-0.17140.05930.4197-0.78230.0250.76110.84960.28950.14630.13640.0448-0.1320.1565-0.04630.2672-14.11513.764-4.221
210.6691-2.0701-8.12715.77345.124519.74960.22180.0633-0.2375-0.2775-0.27230.2056-0.3452-0.32250.05060.19540.009-0.03880.08660.02720.1647-7.1635.391-1.891
36.5712-2.8724-1.5245.62030.18974.1466-0.40560.04320.05320.17170.2463-0.02810.0960.01470.15920.1869-0.0098-0.05350.13480.00120.1642-7.81515.453-1.737
44.3005-0.6166-0.6417.66472.40135.2798-0.22690.24020.1856-0.40350.08120.3306-0.14860.16950.14570.1923-0.0006-0.10450.17460.03230.1812-10.18912.924-7.399
57.86783.70822.623929.69161.54499.2654-0.09240.4972-0.4491-0.55520.2990.98250.3865-0.3124-0.20660.2319-0.0615-0.06630.2876-0.02180.2832-16.3085.251-7.628
65.73472.45010.23746.338-0.09692.2249-0.09990.0456-0.05570.0868-0.1254-0.39810.03750.35360.22520.1783-0.0056-0.04110.17180.05390.18842.11410.1915.161
77.3851.7846-1.28294.1914-0.94684.6838-0.31270.2445-0.0244-0.18390.04110.02290.1458-0.17580.27160.159-0.0276-0.03470.10690.01250.1738-1.53816.0343.409
814.3465-0.2931-9.96487.2583-0.134816.0475-0.12650.50740.0072-0.5341-0.1164-0.4625-0.35610.29960.24280.1816-0.0917-0.07390.21470.06590.20823.76216.831.734
912.6075-7.1427-1.780817.28460.447913.4577-0.0981-1.08490.08750.74590.0026-0.1161-0.4532-0.09180.09550.2175-0.0605-0.0830.26910.01050.15880.56413.65916.084
1010.19641.8169-2.146820.42623.20953.169-0.0114-0.8134-0.61370.0442-0.1303-0.88620.07690.34130.14160.2337-0.0207-0.08860.37540.0660.3418.7810.0410.736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A307 - 315
2X-RAY DIFFRACTION2A316 - 330
3X-RAY DIFFRACTION3A331 - 343
4X-RAY DIFFRACTION4A344 - 368
5X-RAY DIFFRACTION5A369 - 375
6X-RAY DIFFRACTION6B307 - 330
7X-RAY DIFFRACTION7B331 - 342
8X-RAY DIFFRACTION8B343 - 356
9X-RAY DIFFRACTION9B357 - 368
10X-RAY DIFFRACTION10B369 - 375

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