PDB-5uyy: Crystal structure of prephenate dehydrogenase tyrA from Bacillus ...

ID or keywords:

Entry

Database: PDB / ID: 5uyy

Title

Crystal structure of prephenate dehydrogenase tyrA from Bacillus anthracis in complex with L-tyrosine

Components

Prephenate dehydrogenase

Keywords

OXIDOREDUCTASE / 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 / metal ion binding
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Shabalin, I.G. / Hou, J. / Cymborowski, M.T. / Kwon, K. / Christendat, D. / Gritsunov, A.O. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: 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

Deposition	Feb 24, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Apr 7, 2021	Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Oct 4, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5uyy_validation.pdf.gz	472.6 KB	Display	wwPDB validaton report
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Data in CIF	5uyy_validation.cif.gz	79.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uy/5uyy ftp://data.pdbj.org/pub/pdb/validation_reports/uy/5uyy	HTTPS FTP

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Related structure data

Related structure data	5v0sC 6cxdC 6u60C 3gggS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5icg-1 4u6s-1 6v89-1 2zub-d 4gjt-d 5mha-d 2hu2-1 4zp4-2 2r6i-d 6z7t-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP05722

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#61 - Jan 2005 Phenylalanine Hydroxylase similarity (2) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (2) #22 - Oct 2001 Photosystem I similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #127 - Jul 2010 Crystallins similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Prephenate dehydrogenase

B: Prephenate dehydrogenase

C: Prephenate dehydrogenase

D: Prephenate dehydrogenase

hetero molecules

172 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Prephenate dehydrogenase

B: Prephenate dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration, dimer, homology, dimer
85.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Prephenate dehydrogenase

D: Prephenate dehydrogenase

hetero molecules

defined by author&software
85.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.682, 105.588, 179.625
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	THR	THR	A	A	14 - 377	17 - 380
2	1	ARG	ARG	THR	THR	B	B	14 - 377	17 - 380
1	2	GLU	GLU	ILE	ILE	A	A	6 - 378	9 - 381
2	2	GLU	GLU	ILE	ILE	C	C	6 - 378	9 - 381
1	3	ARG	ARG	THR	THR	A	A	14 - 377	17 - 380
2	3	ARG	ARG	THR	THR	D	D	14 - 377	17 - 380
1	4	ARG	ARG	THR	THR	B	B	14 - 377	17 - 380
2	4	ARG	ARG	THR	THR	C	C	14 - 377	17 - 380
1	5	ARG	ARG	ILE	ILE	B	B	14 - 378	17 - 381
2	5	ARG	ARG	ILE	ILE	D	D	14 - 378	17 - 381
1	6	ARG	ARG	THR	THR	C	C	14 - 377	17 - 380
2	6	ARG	ARG	THR	THR	D	D	14 - 377	17 - 380

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Prephenate dehydrogenase Mass: 42707.773 Da / Num. of mol.: 4 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-TYR / TYROSINE Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₁NO₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.67 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 ul of 19 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, and 10 mM BME were mixed with 0.2 ul of the MCSG Suite 1 condition #11 (0.1 M MES pH=6.5, 0.2 M Magnesium ...Details: 0.2 ul of 19 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, and 10 mM BME were mixed with 0.2 ul of the MCSG Suite 1 condition #11 (0.1 M MES pH=6.5, 0.2 M Magnesium chloride, 10% w/v PEG 4000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). His-tag was removed prior to crystallization.

Crystal

Density Matthews: 2.35 Å³/Da / Density % sol: 47.67 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 ul of 19 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, and 10 mM BME were mixed with 0.2 ul of the MCSG Suite 1 condition #11 (0.1 M MES pH=6.5, 0.2 M Magnesium ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2014 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.6→50 Å / Num. obs: 50884 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / B_iso Wilson estimate: 71.2 Å² / R_merge(I) obs: 0.069 / R_pim(I) all: 0.027 / R_rim(I) all: 0.071 / R_sym value: 0.069 / Χ²: 0.978 / Net I/av σ(I): 31.3 / Net I/σ(I): 8.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	Χ²	% possible all	R_rim(I) all
2.6-2.64	7.5	0.963	2.1	2499	0.803	0.374	0.776	100
2.64-2.69	7.6	0.797			0.886	0.309	0.785	100	0.855
2.69-2.74	7.6	0.681			0.905	0.265	0.779	100	0.731
2.74-2.8	7.6	0.561			0.934	0.218	0.79	100	0.602
2.8-2.86	7.5	0.474			0.944	0.185	0.822	100	0.509
2.86-2.93	7.6	0.37			0.966	0.144	0.807	100	0.397
2.93-3	7.5	0.295			0.981	0.115	0.852	100	0.317
3-3.08	7.5	0.24			0.985	0.093	0.902	100	0.257
3.08-3.17	7.5	0.184			0.991	0.072	0.905	100	0.197
3.17-3.28	7.5	0.148			0.994	0.058	0.927	100	0.159
3.28-3.39	7.5	0.11			0.996	0.043	0.952	100	0.119
3.39-3.53	7.5	0.093			0.997	0.037	1.011	100	0.1
3.53-3.69	7.5	0.075			0.998	0.029	0.999	100	0.08
3.69-3.88	7.5	0.064			0.998	0.025	1.072	100	0.069
3.88-4.13	7.5	0.06			0.998	0.024	1.194	100	0.065
4.13-4.45	7.4	0.051			0.999	0.02	1.222	100	0.054
4.45-4.89	7.4	0.044			0.999	0.017	1.303	100	0.048
4.89-5.6	7.3	0.042			0.999	0.016	1.157	100	0.045
5.6-7.05	7.2	0.038			0.999	0.015	1.162	100	0.041
7.05-50	6.5	0.028			0.999	0.012	1.151	99.1	0.031

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing
HKL-3000		phasing
REFMAC	5.8.0107	refinement
PDB_EXTRACT	3.22	data extraction
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3GGG

3ggg

Resolution: 2.6→50 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.929 / SU B: 24.093 / SU ML: 0.266 / SU R Cruickshank DPI: 3.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.285 / ESU R Free: 0.325 / SU R_free Cruickshank DPI: 0.3245
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2461	2466	4.9 %	RANDOM
R_work	0.1886	-	-	-
obs	0.1913	47834	99.93 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 177.83 Å² / B_iso mean: 76.618 Å² / B_iso min: 32.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.39 Å²	0 Å²	-0 Å²
2-	-	-1.19 Å²	0 Å²
3-	-	-	1.58 Å²

Refinement step

Cycle: final / Resolution: 2.6→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11332	0	52	506	11890
B_iso mean	-	-	48.36	61.48	-
Num. residues	-	-	-	-	1476

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	11609
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	11047
X-RAY DIFFRACTION	r_angle_refined_deg	1.732	1.951	15726
X-RAY DIFFRACTION	r_angle_other_deg	1.581	3	25380
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.149	5	1472
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.506	24.363	502
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.361	15	1969
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.182	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1811
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	13098
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	2577

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	38344	0.12
1	2	B	38344	0.12
2	1	A	41848	0.08
2	2	C	41848	0.08
3	1	A	37358	0.12
3	2	D	37358	0.12
4	1	B	38246	0.11
4	2	C	38246	0.11
5	1	B	40058	0.08
5	2	D	40058	0.08
6	1	C	37362	0.12
6	2	D	37362	0.12

LS refinement shell

Resolution: 2.6→2.667 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.359	174	-
R_work	0.283	3486	-
all	-	3660	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.7331	1.4846	-1.5318	4.5865	2.9755	3.4629	-0.5646	-0.443	0.1972	0.4148	-0.1733	1.1275	0.709	0.1048	0.7379	0.8481	0.0846	0.1419	0.3141	0.0815	0.4407	67.646	-43.404	16.69
2	1.8161	0.7545	0.5895	3.8599	0.0009	2.2217	-0.0553	-0.3979	-0.1149	0.4527	0.1973	-0.1418	0.7598	0.3091	-0.142	0.7135	0.2692	0.0007	0.4687	0.0129	0.0267	81.24	-38.349	25.253
3	1.5154	0.6043	0.9874	3.3747	0.8983	2.9226	0.258	-0.1792	-0.1065	0.421	0.1566	-0.3847	0.3687	0.3384	-0.4147	0.4801	0.147	-0.1509	0.3784	-0.2072	0.17	80.86	-9.194	36.488
4	3.9564	-2.2201	-0.4894	4.9205	0.8389	3.7938	0.0407	-0.3351	0.4711	-0.3788	0.4253	-0.7999	-0.2072	0.9401	-0.4661	0.3792	-0.0846	0.1427	0.4616	-0.1926	0.185	87.602	-8.831	4.171
5	1.9023	-0.495	0.9963	6.1072	-0.5263	6.8217	-0.2615	0.277	0.4866	-0.8599	0.274	-0.5983	-0.9734	0.5403	-0.0124	0.6146	-0.1302	-0.0845	0.0992	-0.0315	0.4436	75.425	25.954	18.525
6	1.9238	0.0007	1.1698	3.6254	-0.2554	2.3301	-0.0849	-0.1397	0.339	0.2008	0.1101	0.0749	-0.3316	0.3099	-0.0253	0.469	-0.0113	-0.0404	0.3784	-0.2351	0.2096	75.82	7.963	32.926
7	3.909	1.5683	0.9504	9.215	-3.576	6.6714	0.3251	-0.4927	-0.3369	0.4061	0.1262	0.1087	0.5799	-0.0103	-0.4513	0.472	0.0414	-0.0317	0.4057	-0.1674	0.1889	67.511	-11.189	36.596
8	2.231	-1.5801	-0.3652	5.1139	0.0804	4.5113	0.0013	-0.2319	0.1189	-0.1064	0.0834	0.3311	-0.1794	-0.0824	-0.0847	0.4016	0.0013	-0.0155	0.3432	-0.0865	0.1344	70.124	-11.463	11.557
9	2.9103	1.285	-1.2408	6.1859	2.2292	3.7126	-0.0827	-0.0399	0.207	0.0987	-0.2429	1.6338	0.3819	-0.2102	0.3257	0.4438	-0.0586	-0.0343	0.2186	-0.0221	0.5073	26.379	-31.015	16.586
10	1.2449	0.3671	0.5372	4.0992	-0.3343	2.3072	0.0952	-0.0576	-0.1157	0.3044	-0.0102	0.1821	0.2999	-0.0156	-0.0849	0.5189	0.0076	0.006	0.2754	-0.0085	0.0999	39.602	-26.025	24.962
11	1.1345	0.0844	0.7092	4.433	0.751	2.0065	-0.0442	-0.246	-0.0042	0.197	0.0095	0.3775	0.0392	-0.0385	0.0346	0.5648	0.0041	0.0808	0.2084	-0.0233	0.1069	38.451	3.159	37.147
12	4.1379	-2.1715	-0.7272	6.6235	0.2797	4.1076	-0.0952	-0.2259	0.5587	-0.2819	0.1619	-0.9609	-0.1885	0.5879	-0.0667	0.4859	-0.1023	-0.0562	0.2835	-0.0174	0.2016	44.036	4.486	4.516
13	3.0025	0.9939	1.6221	4.2565	1.2888	7.0772	0.1683	0.3534	0.4311	-0.9181	-0.2842	0.5315	-1.058	0.5679	0.116	1.0018	0.1624	-0.1372	0.1476	0.011	0.2422	31.216	38.485	23.318
14	4.9923	-2.6578	-1.7533	7.3214	2.9002	3.1834	0.1764	0.0697	0.0611	-0.2843	-0.2681	0.5997	-0.5491	-0.3995	0.0917	0.6282	0.1704	-0.2409	0.0781	-0.0861	0.43	23.072	29.499	27.433
15	1.5958	-0.2295	0.4981	4.3247	0.7351	1.4651	-0.0765	-0.1428	-0.051	0.2035	-0.0813	0.4684	0.0313	-0.0447	0.1577	0.5194	-0.0066	0.0436	0.2211	-0.0107	0.1043	35.866	7.504	36.97
16	1.8298	-1.5712	0.4157	5.5998	-1.0038	5.8034	-0.1195	-0.0728	0.0492	-0.1521	0.0957	0.7889	-0.3568	-0.4896	0.0237	0.4049	0.0243	-0.2043	0.2448	-0.0215	0.2997	27.287	0.88	11.975

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 67
2	X-RAY DIFFRACTION	2	A	68 - 194
3	X-RAY DIFFRACTION	3	A	195 - 298
4	X-RAY DIFFRACTION	4	A	299 - 378
5	X-RAY DIFFRACTION	5	B	14 - 96
6	X-RAY DIFFRACTION	6	B	97 - 275
7	X-RAY DIFFRACTION	7	B	276 - 305
8	X-RAY DIFFRACTION	8	B	306 - 378
9	X-RAY DIFFRACTION	9	C	6 - 66
10	X-RAY DIFFRACTION	10	C	67 - 190
11	X-RAY DIFFRACTION	11	C	191 - 295
12	X-RAY DIFFRACTION	12	C	296 - 378
13	X-RAY DIFFRACTION	13	D	14 - 124
14	X-RAY DIFFRACTION	14	D	125 - 183
15	X-RAY DIFFRACTION	15	D	184 - 305
16	X-RAY DIFFRACTION	16	D	306 - 378

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