PDB-3zzh: Crystal structure of the amino acid kinase domain from Saccharomy...

ID or keywords:

Entry

Database: PDB / ID: 3zzh

Title

Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase in complex with its feed- back inhibitor L-arginine

Components

ACETYLGLUTAMATE KINASE

Keywords

TRANSFERASE / ARGININE BIOSYNTHESIS

Function / homology

Function and homology information

Urea cycle / ornithine biosynthetic process / N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / acetylglutamate kinase / acetylglutamate kinase activity / L-arginine biosynthetic process / NADP+ binding / NAD binding / mitochondrial matrix ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

de Cima, S. / Gil-Ortiz, F. / Crabeel, M. / Fita, I. / Rubio, V.

Citation

Journal: Plos One / Year: 2012
Title: Insight on an Arginine Synthesis Metabolon from the Tetrameric Structure of Yeast Acetylglutamate Kinase
Authors: De Cima, S. / Gil-Ortiz, F. / Crabeel, M. / Fita, I. / Rubio, V.

History

Deposition	Sep 1, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 2, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2012	Group: Other
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zzh.cif.gz	471.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3zzh.ent.gz	390.6 KB	Display	PDB format
PDBx/mmJSON format	3zzh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zz/3zzh ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zzh	HTTPS FTP

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Related structure data

Related structure data	3zzfSC 3zzgC 3zziC 4ab7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3zzf-d 3zzg-d 6o42-d 2dfv-d 4lck-2 3u9u-3 4tzw-d 4tzp-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #133 - Jan 2011 Nitric Oxide Synthase similarity (1)

Deposited unit

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

C: ACETYLGLUTAMATE KINASE

D: ACETYLGLUTAMATE KINASE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	69.489, 99.596, 189.238
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.3862, 0.07005, 0.9198), (0.00126, -0.9971, 0.07646), (0.9224, 0.03069, 0.385)	17.32, 43.93, -13.14
2	given	(0.5958, 0.07797, -0.7994), (0.06339, -0.9967, -0.04998), (-0.8007, -0.02089, -0.5988)	-53.37, 37.02, -103.3
3	given	(-0.9701, -0.06672, -0.2336), (-0.05917, 0.9975, -0.03921), (0.2356, -0.02421, -0.9716)	-54.65, -2.007, -100.1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	ACETYLGLUTAMATE KINASE / N-ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / AGK / PROTEIN ...N-ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / AGK / PROTEIN ARG5\ / 6\ / MITOCHONDRIAL Mass: 34015.039 Da / Num. of mol.: 4 / Fragment: AMINO ACID KINASE DOMAIN, RESIDUES 58-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: SIGMA 1278B / Plasmid: PYK6-AAK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01217, acetylglutamate kinase

#1: Protein

ACETYLGLUTAMATE KINASE / N-ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / AGK / PROTEIN ...

Mass: 34015.039 Da / Num. of mol.: 4 / Fragment: AMINO ACID KINASE DOMAIN, RESIDUES 58-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: SIGMA 1278B / Plasmid: PYK6-AAK / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01217, acetylglutamate kinase

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Non-polymers , 7 types, 556 molecules

#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₂O₄
#5: Chemical	ChemComp-NLG / N-ACETYL-L-GLUTAMATE Mass: 189.166 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₁₁NO₅
#6: Chemical	ChemComp-ARG / ARGININE Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.41 Å³/Da / Density % sol: 49 % / Description: NONE
Crystal grow	pH: 4.6 Details: PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE (NAG); 24 HOURS BEFORE FREEZING ARGININE 0.2 M WAS ADDED TO ...Details: PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE (NAG); 24 HOURS BEFORE FREEZING ARGININE 0.2 M WAS ADDED TO CRYSTALLIZATION DROP. 20% GLYCEROL WAS USED AS CRYOPROTECTOR

Crystal

Density Matthews: 2.41 Å³/Da / Density % sol: 49 % / Description: NONE

Crystal grow

pH: 4.6
Details: PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE (NAG); 24 HOURS BEFORE FREEZING ARGININE 0.2 M WAS ADDED TO ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9786
Detector	Type: ADSC CCD / Detector: CCD / Date: Sep 7, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.1→20 Å / Num. obs: 77012 / % possible obs: 99.6 % / Observed criterion σ(I): 1.9 / Redundancy: 4.8 % / B_iso Wilson estimate: 19.8 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 3.8
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZZF

3zzf

Resolution: 2.1→20 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.925 / SU B: 8.639 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21544	3860	5 %	RANDOM
R_work	0.18037	-	-	-
obs	0.18211	72907	99.27 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.225 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.32 Å²	0 Å²	0 Å²
2-	-	0.26 Å²	0 Å²
3-	-	-	0.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8953	0	276	497	9726

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	9417
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6462
X-RAY DIFFRACTION	r_angle_refined_deg	1.019	1.988	12645
X-RAY DIFFRACTION	r_angle_other_deg	0.801	3.005	15521
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.699	5	1179
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.555	24.987	389
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.565	15	1696
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.913	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	1470
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10300
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1737
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.326	1.5	5829
X-RAY DIFFRACTION	r_mcbond_other	0.061	1.5	2402
X-RAY DIFFRACTION	r_mcangle_it	0.649	2	9418
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.143	3	3588
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.003	4.5	3227
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	312	-
R_work	0.215	5240	-
obs	-	-	99.87 %

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	3.6237	0.0189	3.1064	3.2823	0.042	9.3537	0.3071	-0.4284	-0.2794	0.0333	0.1276	0.1501	0.6002	-0.3335	-0.4347	0.1142	-0.0185	-0.1414	0.1407	0.0797	0.2535	-19.356	-2.192	-47.468
2	2.7552	0.6588	-0.4891	2.616	0.6717	2.4237	-0.0534	0.1456	0.0395	-0.1112	0.1082	-0.0444	0.085	-0.0116	-0.0549	0.1161	-0.0033	-0.0077	0.0496	0.0229	0.0545	-14.715	40.274	-50.831
3	3.7566	-0.3397	3.3326	1.0764	0.2961	5.2025	-0.2996	-0.3257	0.2895	0.2007	-0.0462	0.096	-0.8659	-0.2581	0.3457	0.3479	0.0081	-0.015	0.1146	-0.0273	0.1413	-27.424	40.484	-60.202
4	5.2624	-0.7965	1.0134	3.7535	1.1485	6.4857	0.0515	0.1453	-0.247	-0.0048	0.0853	-0.2663	0.2142	0.2832	-0.1369	0.0721	0.0183	-0.0849	0.1045	0.0334	0.209	-20.077	-1.464	-60.828
5	1.2074	-0.3759	0.3015	1.5752	0.1049	1.0937	-0.0728	-0.1464	0.0041	0.076	0.0818	-0.0574	0.0365	0.0212	-0.009	0.0905	0.0518	-0.0183	0.0592	-0.0011	0.1115	-1.671	9.907	-30.057
6	0.8219	-0.2136	0.1557	1.1132	0.0654	1.339	-0.0326	-0.1117	0.0218	0.1317	0.0968	-0.1229	0.0761	0.1196	-0.0642	0.0979	0.0516	-0.0235	0.0509	-0.0291	0.0894	-8.541	32.164	-26.405
7	0.9501	0.1108	-0.0278	0.6333	-0.5005	2.6407	0.0433	0.0829	0.0958	0.0069	0.018	0.0091	-0.122	0.0316	-0.0613	0.0796	-0.0238	0.0041	0.0441	0.0233	0.1001	-29.624	28.968	-83.987
8	0.9886	0.0054	0.1249	1.1102	-0.5607	1.4397	-0.0228	0.1442	0.0217	-0.1323	0.0718	-0.0384	0.0692	-0.0052	-0.0489	0.056	-0.0309	-0.011	0.0387	0.0192	0.096	-35.878	6.575	-80.822
9	2.0518	-1.356	0.8519	3.6286	-0.6322	2.9568	-0.0825	-0.2477	-0.2251	-0.0207	0.1608	0.2617	0.2733	-0.0915	-0.0784	0.1278	0.0318	0.0199	0.0779	0.0597	0.1403	-2.135	-10.095	-29.428
10	2.9554	0.0279	0.5911	2.2663	2.0421	3.6305	-0.035	-0.1344	0.2516	-0.0405	0.1908	-0.2746	-0.1261	0.3058	-0.1559	0.0853	0.002	-0.0164	0.0402	-0.0475	0.1603	-7.72	51.858	-28.482
11	6.1665	1.9343	2.2634	5.3518	-0.7872	5.2317	-0.9	0.7796	0.9375	-0.3925	0.3019	0.3328	-1.2975	-0.0073	0.5981	0.6188	-0.0788	-0.1853	0.1225	0.0902	0.3064	-31.517	49.819	-81.188
12	2.333	1.6038	0.4246	2.9023	0.9292	3.2399	-0.0871	0.2724	-0.3117	-0.2046	0.1009	-0.3335	0.2747	0.0802	-0.0138	0.1377	0.0118	0.0229	0.0367	-0.0205	0.1717	-33.725	-13.197	-80.528

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	62 - 98
2	X-RAY DIFFRACTION	2	B	63 - 98
3	X-RAY DIFFRACTION	3	C	63 - 98
4	X-RAY DIFFRACTION	4	D	63 - 98
5	X-RAY DIFFRACTION	5	A	99 - 271
6	X-RAY DIFFRACTION	6	B	99 - 271
7	X-RAY DIFFRACTION	7	C	99 - 271
8	X-RAY DIFFRACTION	8	D	99 - 271
9	X-RAY DIFFRACTION	9	A	272 - 357
10	X-RAY DIFFRACTION	10	B	272 - 357
11	X-RAY DIFFRACTION	11	C	272 - 357
12	X-RAY DIFFRACTION	12	D	272 - 357

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