PDB-6hwk: Glucosamine kinase (crystal form B)

ID or keywords:

Entry

Database: PDB / ID: 6hwk

Title

Glucosamine kinase (crystal form B)

Components

Glucosamine kinase

Keywords

TRANSFERASE / Glucosamine kinase

Function / homology

glucosamine kinase / Glucosamine kinase / glucosamine kinase activity / carbohydrate metabolic process / phosphorylation / Protein kinase-like domain superfamily / magnesium ion binding / ATP binding / Glucosamine kinase

Function and homology information

Biological species

Streptacidiphilus jiangxiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.688 Å

Authors

Manso, J.A. / Pereira, P.J.B.

Citation

Journal: mBio / Year: 2019
Title: Molecular Fingerprints for a Novel Enzyme Family in with Glucosamine Kinase Activity.
Authors: José A Manso / Daniela Nunes-Costa / Sandra Macedo-Ribeiro / Nuno Empadinhas / Pedro José Barbosa Pereira /

Abstract: have long been the main source of antibiotics, secondary metabolites with tightly controlled biosynthesis by environmental and physiological factors. Phosphorylation of exogenous glucosamine has ... have long been the main source of antibiotics, secondary metabolites with tightly controlled biosynthesis by environmental and physiological factors. Phosphorylation of exogenous glucosamine has been suggested as a mechanism for incorporation of this extracellular material into secondary metabolite biosynthesis, but experimental evidence of specific glucosamine kinases in is lacking. Here, we present the molecular fingerprints for the identification of a unique family of actinobacterial glucosamine kinases. Structural and biochemical studies on a distinctive kinase from the soil bacterium unveiled its preference for glucosamine and provided structural evidence of a phosphoryl transfer to this substrate. Conservation of glucosamine-contacting residues across a large number of uncharacterized actinobacterial proteins unveiled a specific glucosamine binding sequence motif. This family of kinases and their genetic context may represent the missing link for the incorporation of environmental glucosamine into the antibiotic biosynthesis pathways in and can be explored to enhance antibiotic production. The discovery of novel enzymes involved in antibiotic biosynthesis pathways is currently a topic of utmost importance. The high levels of antibiotic resistance detected worldwide threaten our ability to combat infections and other 20th-century medical achievements, namely, organ transplantation or cancer chemotherapy. We have identified and characterized a unique family of enzymes capable of phosphorylating glucosamine to glucosamine-6-phosphate, a crucial molecule directly involved in the activation of antibiotic production pathways in , nature's main source of antimicrobials. The consensus sequence identified for these glucosamine kinases will help establish a molecular fingerprint to reveal yet-uncharacterized sequences in antibiotic producers, which should have an important impact in biotechnological and biomedical applications, including the enhancement and optimization of antibiotic production.

History

Deposition	Oct 12, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 1, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Dec 11, 2019	Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.3	Sep 30, 2020	Group: Database references / Derived calculations / Refinement description Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / software / struct_conn Item: _citation.title / _citation_author.identifier_ORCID ..._citation.title / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _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.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
Revision 1.4	May 1, 2024	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6hwk.cif.gz	611.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6hwk.ent.gz	505.5 KB	Display	PDB format
PDBx/mmJSON format	6hwk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6hwk_validation.pdf.gz	460.7 KB	Display	wwPDB validaton report
Full document	6hwk_full_validation.pdf.gz	467.9 KB	Display
Data in XML	6hwk_validation.xml.gz	54.4 KB	Display
Data in CIF	6hwk_validation.cif.gz	75.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hw/6hwk ftp://data.pdbj.org/pub/pdb/validation_reports/hw/6hwk	HTTPS FTP

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Related structure data

Related structure data	SASDEL6C SASDEM6C SASDEN6C SASDEP6C SASDEQ6C SASDER6C 6hwjC 6hwlC C: citing same article (ref.)
Similar structure data	4r11-d 5ekq-d 5lt2-d 4xoa-d 4mmz-d 4egq-d 10319 4uim-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15785/SBGRID/615 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glucosamine kinase

B: Glucosamine kinase

C: Glucosamine kinase

D: Glucosamine kinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, The glucosamine kinase is a monomer as determined by SAXS and gel-filtration

Unit cell

Length a, b, c (Å)	58.202, 111.216, 150.589
Angle α, β, γ (deg.)	90.00, 93.21, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glucosamine kinase / Glucosamine kinase Mass: 48308.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptacidiphilus jiangxiensis (bacteria) Gene: SAMN05414137_114149 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H7TQR5
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.52 Å³/Da / Density % sol: 51.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH 5.7, 16.5% (wt/vol) PEG 3350, 0.15 M MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 2, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 2.688→47.274 Å / Num. obs: 52817 / % possible obs: 98.9 % / Redundancy: 6.9 % / B_iso Wilson estimate: 41.8 Å² / CC_1/2: 0.986 / R_merge(I) obs: 0.208 / R_pim(I) all: 0.085 / R_rim(I) all: 0.225 / Net I/σ(I): 9.6
Reflection shell	Resolution: 2.69→2.74 Å / Redundancy: 7.2 % / R_merge(I) obs: 1.17 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2664 / CC_1/2: 0.59 / R_pim(I) all: 0.469 / R_rim(I) all: 1.262 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: D_1200012387

Resolution: 2.688→47.274 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.76

	R_factor	Num. reflection	% reflection
R_free	0.2416	2646	5.01 %
R_work	0.2055	-	-
obs	0.2073	52795	98.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.688→47.274 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12113	0	7	256	12376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	12387
X-RAY DIFFRACTION	f_angle_d	0.45	16991
X-RAY DIFFRACTION	f_dihedral_angle_d	13.66	7340
X-RAY DIFFRACTION	f_chiral_restr	0.038	1980
X-RAY DIFFRACTION	f_plane_restr	0.004	2238

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6883-2.7372	0.3221	124	0.2726	2655	X-RAY DIFFRACTION	100
2.7372-2.7898	0.3441	151	0.2641	2666	X-RAY DIFFRACTION	100
2.7898-2.8468	0.3075	133	0.264	2649	X-RAY DIFFRACTION	100
2.8468-2.9087	0.2804	159	0.2628	2644	X-RAY DIFFRACTION	100
2.9087-2.9763	0.3143	136	0.2564	2615	X-RAY DIFFRACTION	100
2.9763-3.0507	0.3309	134	0.253	2660	X-RAY DIFFRACTION	99
3.0507-3.1332	0.3499	143	0.2646	2602	X-RAY DIFFRACTION	99
3.1332-3.2254	0.2959	153	0.2524	2661	X-RAY DIFFRACTION	99
3.2254-3.3295	0.2776	136	0.2251	2585	X-RAY DIFFRACTION	99
3.3295-3.4484	0.2479	142	0.219	2615	X-RAY DIFFRACTION	98
3.4484-3.5864	0.2645	141	0.2145	2592	X-RAY DIFFRACTION	97
3.5864-3.7496	0.2396	124	0.2029	2560	X-RAY DIFFRACTION	97
3.7496-3.9472	0.2111	113	0.1864	2539	X-RAY DIFFRACTION	94
3.9472-4.1944	0.2085	141	0.1617	2659	X-RAY DIFFRACTION	100
4.1944-4.518	0.1846	150	0.1625	2669	X-RAY DIFFRACTION	100
4.518-4.9722	0.2098	142	0.1708	2663	X-RAY DIFFRACTION	100
4.9722-5.6906	0.2284	132	0.2027	2706	X-RAY DIFFRACTION	100
5.6906-7.1656	0.2145	151	0.2088	2687	X-RAY DIFFRACTION	100
7.1656-47.2815	0.1737	141	0.1684	2722	X-RAY DIFFRACTION	99

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	1.9261	-0.3322	0.1005	1.5184	-0.5065	3.0109	0.1724	0.67	-0.0174	-0.3312	-0.1978	-0.0658	-0.2465	0.7619	0.0101	0.392	0.0254	0.0295	0.6216	0.0412	0.3372	-34.5052	39.8459	-39.2554
2	0.6644	0.3379	0.2771	2.2331	0.0977	1.4225	0.0529	0.0147	0.0697	0.0314	-0.0641	0.1162	-0.0073	-0.064	0.0213	0.2314	-0.0059	0.0326	0.2432	0.0145	0.2185	-53.4879	25.5253	-18.4725
3	2.1785	-0.3394	0.7307	1.4761	0.0689	2.5327	-0.5803	-0.5403	0.4735	0.5956	0.1047	-0.4281	-0.9673	0.2907	0.4476	0.8554	0.1277	-0.2614	0.481	0.1013	0.6649	-58.3733	-42.3338	-21.706
4	6.0871	0.984	1.3231	3.859	-0.5793	4.5257	-0.4118	0.4772	0.6757	0.7858	-0.3061	-1.0673	-0.5051	1.1629	0.6953	0.5724	-0.0616	-0.1657	0.5893	0.3252	0.7907	-54.0441	-42.1658	-36.0803
5	3.2081	-0.7156	0.2093	3.4735	1.9281	6.0884	-0.3409	-0.5745	-0.1856	0.8544	0.1858	0.067	0.1316	-0.2822	0.185	0.5161	0.1377	0.0235	0.3809	0.0187	0.4788	-71.5206	-44.436	-33.4437
6	1.478	-1.3688	2.2716	4.3255	-0.3731	5.0405	-0.123	0.0634	0.2735	0.4873	-0.1416	-0.2281	0.1714	0.3814	0.2357	0.3097	0.0313	0.0373	0.2723	0.0346	0.3978	-63.5713	-45.7248	-38.84
7	2.6169	1.3052	-2.0699	4.0991	-2.8619	6.3107	0.2328	-0.0474	-0.1523	-0.1571	-0.2838	-0.2971	0.2183	0.6924	0.0802	0.2693	0.0396	0.0233	0.3128	-0.0662	0.3571	-68.2021	-39.5106	-60.3029
8	0.0146	-0.0397	0.0405	5.4609	-2.5251	1.2822	0.1927	-0.0601	-0.2644	0.6473	0.1146	1.3111	-0.103	-0.2487	-0.2739	0.3903	-0.0164	0.1514	0.4462	0.074	0.6019	-91.222	-33.842	-44.3323
9	1.8053	0.753	0.7298	8.5561	-2.5066	3.2419	0.2797	-0.2692	-0.1187	-0.4858	-0.3448	0.9965	0.1995	0.1101	0.0648	0.2365	0.0209	0.0542	0.4316	0.0585	0.4208	-93.978	-27.2278	-54.7769
10	3.8148	3.521	-1.2019	3.3412	-1.426	4.6731	-0.2764	-0.2936	-0.3336	-0.2146	0.099	0.0956	0.5984	0.4318	0.2265	0.3915	0.11	0.0365	0.2147	0.0175	0.4071	-73.2691	-42.1895	-49.4584
11	0.9764	0.4447	-0.5298	3.1123	-1.8713	1.6009	0.0055	0.0087	-0.155	-0.0991	0.0343	0.1545	0.0981	-0.0682	-0.0436	0.2517	0.0253	0.0233	0.2675	-0.0299	0.3184	-76.1088	-36.6391	-55.7364
12	2.1466	-0.084	-0.2067	1.7622	-0.4122	1.3025	-0.0749	0.1693	0.1134	0.0175	0.2569	0.4579	0.1165	-0.0921	-0.1577	0.2751	0.0296	0.0284	0.3066	0.0561	0.3038	-84.3143	-35.4489	-51.7795
13	9.2344	2.0716	3.6777	2.1532	0.3302	6.6118	0.2955	0.5368	-0.5621	-0.3119	0.0189	-0.422	0.3767	0.1957	-0.2675	0.3166	0.0291	0.056	0.2431	0.0089	0.2833	-82.7187	-25.1453	-59.2849
14	1.3901	-0.6676	0.4265	1.3798	0.267	4.9123	0.1293	0.2157	-0.1146	-0.4106	0.0456	0.0286	0.3263	0.1172	-0.1814	0.3216	-0.0261	-0.0113	0.3461	0.0799	0.3581	-40.7085	-14.9813	-78.748
15	2.1878	0.6517	-0.4942	1.9262	-0.4875	1.2047	0.1082	0.035	0.3476	0.1187	-0.0662	0.1009	-0.3098	0.0118	-0.0372	0.351	-0.0093	0.0384	0.2644	0.0113	0.3344	-59.9964	0.6739	-60.5005
16	0.5595	0.2302	-0.0686	0.9189	-1.308	6.2845	-0.0527	0.0509	-0.0091	0.2077	0.103	0.0278	-0.1528	0.0734	-0.0546	0.2928	0.0086	0.0085	0.2459	-0.0083	0.3602	-16.4247	-2.0418	-4.0644
17	1.5078	-0.5939	-0.0084	1.3159	-0.2495	1.3551	0.0447	0.1775	-0.0746	-0.1049	0.0157	0.0873	0.2273	-0.0298	-0.0594	0.3108	-0.0453	0.0036	0.2537	-0.0089	0.25	-35.176	-9.9965	-27.4292

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 193 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 194 through 436 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 3 through 102 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 103 through 134 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 135 through 157 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 158 through 193 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 194 through 236 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 237 through 265 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 266 through 288 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 289 through 315 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 316 through 387 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 388 through 416 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 417 through 435 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 4 through 193 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 194 through 433 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 3 through 193 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 194 through 434 )

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