PDB-7mqv: Crystal structure of truncated (ACT domain removed) prephenate de...

ID or keywords:

Entry

Database: PDB / ID: 7mqv

Title

Crystal structure of truncated (ACT domain removed) prephenate dehydrogenase tyrA from Bacillus anthracis in complex with NAD

Components

Prephenate dehydrogenase

Keywords

HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

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 /

FOURIER SYNTHESIS / Resolution: 2.4 Å

Authors

Shabalin, I.G. / Gritsunov, A. / Gabryelska, A. / Czub, M.P. / Grabowski, M. / Cooper, D.R. / Christendat, D. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: The crystal structure of Bacillus anthracis prephenate dehydrogenase identified an ACT regulatory domain and a novel mode of metabolic regulation for proteins within the prephenate dehydrogenase family of enzyme
Authors: Shabalin, I.G. / Hou, J. / Christendat, D. / Minor, W.

History

Deposition	May 6, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 19, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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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Download

PDBx/mmCIF format	7mqv.cif.gz	476.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7mqv.ent.gz	392.5 KB	Display	PDB format
PDBx/mmJSON format	7mqv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7mqv_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	7mqv_full_validation.pdf.gz	1.6 MB	Display
Data in XML	7mqv_validation.xml.gz	42.6 KB	Display
Data in CIF	7mqv_validation.cif.gz	59.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mq/7mqv ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mqv	HTTPS FTP

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Related structure data

Related structure data	6u60S S: Starting model for refinement
Similar structure data	7mqv-2 4uaf-d 5env-d 3ma6-d 6kuy-d 6awv-d 1vpv-d 4re1-d 5u5n-d 5vkt-2 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 (3) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (3) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: Prephenate dehydrogenase

B: Prephenate dehydrogenase

C: Prephenate dehydrogenase

D: Prephenate dehydrogenase

hetero molecules

141 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
70.3 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
70.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.774, 118.882, 75.558
Angle α, β, γ (deg.)	90.000, 92.390, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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	PRO	PRO	A	A	14 - 296	17 - 299
2	1	ARG	ARG	PRO	PRO	B	B	14 - 296	17 - 299
1	2	SER	SER	PRO	PRO	A	A	7 - 296	10 - 299
2	2	SER	SER	PRO	PRO	C	C	7 - 296	10 - 299
1	3	MET	MET	PRO	PRO	A	A	13 - 296	16 - 299
2	3	MET	MET	PRO	PRO	D	D	13 - 296	16 - 299
1	4	ARG	ARG	VAL	VAL	B	B	14 - 297	17 - 300
2	4	ARG	ARG	VAL	VAL	C	C	14 - 297	17 - 300
1	5	ARG	ARG	ARG	ARG	B	B	14 - 298	17 - 301
2	5	ARG	ARG	ARG	ARG	D	D	14 - 298	17 - 301
1	6	MET	MET	VAL	VAL	C	C	13 - 297	16 - 300
2	6	MET	MET	VAL	VAL	D	D	13 - 297	16 - 300

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Prephenate dehydrogenase Mass: 34500.414 Da / Num. of mol.: 4 / Mutation: ACT domain truncated (1-306 are present) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: tyrA, GBAA_2954 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-codonplus-RIL / References: UniProt: Q81P63, prephenate dehydrogenase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.73 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 ul of 6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 5 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #46 (20%w/v PEG 3350, 0. ...Details: 0.2 ul of 6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 5 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #46 (20%w/v PEG 3350, 0.2M Li citrate ) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci).

Crystal

Density Matthews: 2.4 Å³/Da / Density % sol: 48.73 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 5 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #46 (20%w/v PEG 3350, 0. ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97929 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97929 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 51186 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / R_merge(I) obs: 0.114 / R_pim(I) all: 0.076 / R_rim(I) all: 0.137 / R_sym value: 0.114 / Χ²: 0.867 / Net I/σ(I): 5.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	R_sym value	Χ²	% possible all
2.4-2.44	2.9	0.866	2508	0.481	0.591	1.053	0.866	0.807	98.2
2.44-2.49	3	0.772	2518	0.567	0.521	0.935		0.844	99.4
2.49-2.53	3	0.746	2551	0.569	0.505	0.904		0.859	99.6
2.53-2.59	3.1	0.645	2544	0.648	0.435	0.78		0.85	99.8
2.59-2.64	3.1	0.633	2564	0.645	0.428	0.767		0.905	99.7
2.64-2.7	3.1	0.58	2523	0.654	0.393	0.703		0.956	99.7
2.7-2.77	3.1	0.463	2581	0.756	0.312	0.56		0.918	99.8
2.77-2.85	3.1	0.383	2540	0.816	0.257	0.463		0.917	99.6
2.85-2.93	3.1	0.335	2569	0.864	0.225	0.405		0.936	99.8
2.93-3.02	3.2	0.275	2534	0.9	0.184	0.332		0.951	99.7
3.02-3.13	3.1	0.226	2554	0.919	0.152	0.274		0.934	99.6
3.13-3.26	3.2	0.174	2552	0.955	0.116	0.21		0.927	99.8
3.26-3.41	3.2	0.14	2558	0.97	0.093	0.169		0.94	99.9
3.41-3.58	3.2	0.104	2585	0.977	0.07	0.126		0.921	100
3.58-3.81	3.2	0.084	2550	0.986	0.057	0.102		0.902	100
3.81-4.1	3.2	0.068	2578	0.99	0.045	0.082		0.892	100
4.1-4.52	3.1	0.052	2587	0.992	0.035	0.063		0.862	100
4.52-5.17	3.1	0.045	2564	0.994	0.03	0.054		0.811	100
5.17-6.51	3.1	0.046	2590	0.992	0.031	0.056		0.619	99.9
6.51-50	3.1	0.028	2636	0.997	0.019	0.034		0.583	99.9

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction
HKL-3000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 6U60

6u60

Resolution: 2.4→49.12 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.933 / SU B: 18.091 / SU ML: 0.203 / SU R Cruickshank DPI: 0.6184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.618 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2155	2131	4.7 %	RANDOM
R_work	0.167	-	-	-
obs	0.1692	42767	88.15 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 209.96 Å² / B_iso mean: 46.649 Å² / B_iso min: 18.07 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	-0 Å²	0.43 Å²
2-	-	0.06 Å²	0 Å²
3-	-	-	0.17 Å²

Refinement step

Cycle: final / Resolution: 2.4→49.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9095	0	183	286	9564
B_iso mean	-	-	37.15	39.45	-
Num. residues	-	-	-	-	1160

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	9488
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	8877
X-RAY DIFFRACTION	r_angle_refined_deg	1.441	1.627	12855
X-RAY DIFFRACTION	r_angle_other_deg	1.287	1.593	20555
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.055	5	1156
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.958	23.826	447
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.742	15	1657
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.433	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1252
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10854
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1962

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	8658	0.1
1	2	B	8658	0.1
2	1	A	8887	0.1
2	2	C	8887	0.1
3	1	A	8875	0.07
3	2	D	8875	0.07
4	1	B	8671	0.09
4	2	C	8671	0.09
5	1	B	8664	0.1
5	2	D	8664	0.1
6	1	C	8873	0.08
6	2	D	8873	0.08

LS refinement shell

Resolution: 2.4→2.462 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.273	93	-
R_work	0.268	1765	-
all	-	1858	-
obs	-	-	49.15 %

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	3.3305	-7.268	-4.2509	16.4212	9.568	5.5789	-0.2605	-0.2245	-0.0832	0.3393	-0.0081	0.4878	0.2327	0.0156	0.2686	0.4664	0.0781	0.0251	0.7001	-0.1474	0.3998	-20.275	90.247	32.366
2	5.6329	1.5282	0.7799	2.6992	1.2814	3.0577	0.1942	-0.6058	-0.3059	0.5202	0.0268	-0.2172	0.097	0.1665	-0.221	0.1729	0.0224	-0.0341	0.1358	0.0035	0.0806	-13.246	73.361	19.483
3	5.2914	-0.7334	0.6219	3.3216	0.7292	3.2527	-0.0501	0.1494	0.3332	-0.0826	0.0927	-0.0717	-0.1809	0.2364	-0.0426	0.1288	-0.0143	0.0218	0.1331	0.0042	0.0649	-14.718	80.529	8.405
4	9.9151	-3.202	-2.1525	2.0615	0.6871	1.8239	0.1948	-0.042	0.0131	-0.0705	-0.1696	-0.0929	-0.0088	0.2798	-0.0253	0.0846	-0.0114	-0.0155	0.1489	-0.0018	0.016	0.864	63.83	-4.576
5	3.3051	1.0727	-1.8694	1.573	-0.2228	2.9405	-0.0241	0.2751	0.1891	-0.1652	0.0255	0.1373	-0.1999	-0.2317	-0.0014	0.0684	0.0406	-0.0495	0.226	0.0229	0.0579	-5.312	67.854	-18.244
6	3.945	-0.5835	0.7781	2.6004	-0.7867	2.6471	-0.1306	-0.0215	0.8722	0.1719	-0.0756	-0.4303	-0.5898	0.1656	0.2062	0.2136	-0.0056	-0.1137	0.1186	-0.0719	0.3844	29.535	85.645	-21.912
7	5.5008	1.2641	-0.5992	4.6244	-0.725	6.6904	-0.0412	0.3019	0.4344	-0.2406	0.0495	-0.2864	-0.1214	0.0986	-0.0082	0.0732	0.0258	-0.0365	0.0923	-0.0012	0.1204	29.913	71.499	-28.67
8	4.1125	-0.854	-0.6061	4.7502	1.1996	2.2077	-0.0037	-0.3868	0.4952	0.2492	-0.0315	-0.0159	-0.2612	-0.0743	0.0352	0.1251	0.0103	-0.0416	0.1965	-0.0589	0.0824	28.974	71.117	-14.482
9	12.9914	-7.3617	-3.3353	6.1703	1.8647	2.1949	0.0419	-0.1028	0.3116	0.1226	0.1142	0.0658	-0.2751	-0.1692	-0.156	0.152	-0.0251	0.0126	0.1789	0.0363	0.0459	1.464	70.375	-14.256
10	2.9652	0.1269	-0.7175	1.644	-0.4573	2.9625	-0.0349	-0.1165	-0.1468	0.0764	0.0444	-0.003	0.0782	0.0329	-0.0094	0.0185	0.0299	-0.0174	0.1127	-0.011	0.0472	3.081	60.274	-11.438
11	5.6898	3.5899	-1.1285	6.8548	-0.8661	0.8546	-0.1109	0.0373	-0.5639	0.0949	0.0408	0.3268	0.3311	-0.3532	0.07	0.2547	-0.1186	-0.0419	0.2252	-0.033	0.2101	-8.263	35.813	28.647
12	5.9487	1.5913	-0.2227	11.9699	1.1109	9.3009	-0.083	0.38	0.3232	-0.4788	0.0458	0.4842	-0.3819	-0.7023	0.0372	0.1269	0.0426	-0.1231	0.2847	0.0044	0.2221	-9.06	48.483	21.561
13	3.5651	-0.0872	-0.0914	2.5691	0.0677	3.4625	-0.0556	-0.0901	-0.2139	0.0338	-0.0352	0.1736	0.1843	-0.1104	0.0907	0.0617	-0.0266	-0.0054	0.0938	0.0278	0.0492	3.061	43.211	34.964
14	1.5737	0.5309	-2.0827	0.5141	-1.2348	6.9053	0.0036	0.1451	0.0117	-0.0733	-0.1045	-0.0645	-0.1087	0.0445	0.1009	0.063	0.024	-0.0151	0.1286	0.0154	0.0607	20.234	55.195	18.2
15	2.6461	-1.0987	-2.204	2.5709	1.4426	3.8167	0.0118	-0.2976	-0.2916	0.1563	-0.1206	-0.0633	0.2239	0.2536	0.1087	0.0685	0.0062	-0.0432	0.2137	0.0724	0.0691	35.298	50.115	23.05
16	7.8155	1.1422	1.1399	4.6132	-0.5493	6.6609	0.0106	0.5209	-0.6148	-0.5204	-0.0506	0.0662	0.3882	-0.0274	0.0399	0.1182	0.0035	-0.0071	0.1082	-0.0141	0.1702	35.787	35.849	-11.745
17	2.0967	1.1329	-0.0449	3.6852	0.6695	2.3467	-0.0104	0.0277	-0.5321	-0.159	-0.0771	-0.4799	0.3031	0.2045	0.0876	0.0726	0.0564	0.0212	0.1743	0.0104	0.1618	45.602	40.074	-8.616
18	2.8304	0.7322	-0.4731	4.8624	-0.7758	4.5705	-0.0566	0.0939	-0.1565	-0.051	-0.0282	0.0462	0.114	-0.0697	0.0848	0.0246	0.0366	-0.0132	0.1031	-0.0324	0.0276	33.65	48.193	-9.427
19	2.5878	1.1084	-2.9948	1.9972	-2.0726	6.248	-0.1116	-0.2613	-0.3053	0.1586	0.0244	0.1397	0.2201	-0.1311	0.0873	0.0896	0.0161	0.0133	0.1838	0.0457	0.1113	31.948	47.833	16.489
20	4.2769	0.0539	-1.7083	0.6654	-0.281	2.5907	0.0679	0.0541	0.1479	0.0018	-0.0084	0.0457	-0.2163	-0.1497	-0.0594	0.0598	0.0118	-0.0105	0.063	0.0264	0.0238	24.455	61.004	16.229

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 16
2	X-RAY DIFFRACTION	2	A	17 - 122
3	X-RAY DIFFRACTION	3	A	123 - 188
4	X-RAY DIFFRACTION	4	A	189 - 248
5	X-RAY DIFFRACTION	5	A	249 - 297
6	X-RAY DIFFRACTION	6	B	14 - 64
7	X-RAY DIFFRACTION	7	B	65 - 138
8	X-RAY DIFFRACTION	8	B	139 - 185
9	X-RAY DIFFRACTION	9	B	186 - 237
10	X-RAY DIFFRACTION	10	B	238 - 299
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