PDB-8vhu: Crystal structure of dATP bound E. coli class Ia ribonucleotide r...

ID or keywords:

Entry

Database: PDB / ID: 8vhu

Title

Crystal structure of dATP bound E. coli class Ia ribonucleotide reductase alpha construct fused with the C-terminal tail of E. coli class Ia beta subunit

Components

Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta

Keywords

OXIDOREDUCTASE / Ribonucleotide reductase / allosteric regulation / nucleotide binding / subunit interaction

Function / homology

Function and homology information

ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / iron ion binding / ATP binding ...
Similarity search - Function

Biological species

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 Å

Authors

Funk, M.A. / Zimanyi, C.M. / Drennan, C.L.

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35GM126982	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	T32GM08334	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P30-ES002109	United States
National Science Foundation (NSF, United States)	0645960	United States

Citation

Journal: Biochemistry / Year: 2024
Title: How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase.
Authors: Funk, M.A. / Zimanyi, C.M. / Andree, G.A. / Hamilos, A.E. / Drennan, C.L.

History

Deposition	Jan 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 4, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Database references / Structure summary / Category: citation / pdbx_entry_details Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vhu.cif.gz	633.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8vhu.ent.gz	514.3 KB	Display	PDB format
PDBx/mmJSON format	8vhu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vhu_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8vhu_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8vhu_validation.xml.gz	75 KB	Display
Data in CIF	8vhu_validation.cif.gz	104.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vh/8vhu ftp://data.pdbj.org/pub/pdb/validation_reports/vh/8vhu	HTTPS FTP

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Related structure data

Related structure data	8vhnC 8vhoC 8vhpC 8vhqC 8vhrC 1r1rS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	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	#238 - Oct 2019 Ribonucleotide Reductase similarity (22) #177 - Sep 2014 Apoptosomes similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta

B: Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	88.214, 111.207, 209.701
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta Mass: 90940.352 Da / Num. of mol.: 2 Mutation: Truncated final 8 residues of alpha,fused C-terminal 35 residues of beta Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: nrdA, dnaF, b2234, JW2228, nrdB, ftsB, b2235, JW2229 / Production host: Escherichia coli (E. coli) References: UniProt: P00452, UniProt: P69924, ribonucleoside-diphosphate reductase

#1: Protein

Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta

Mass: 90940.352 Da / Num. of mol.: 2
Mutation: Truncated final 8 residues of alpha,fused C-terminal 35 residues of beta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: nrdA, dnaF, b2234, JW2228, nrdB, ftsB, b2235, JW2229 / Production host:

Escherichia coli (E. coli)
References: UniProt: P00452, UniProt: P69924, ribonucleoside-diphosphate reductase

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Non-polymers , 6 types, 1371 molecules

#2: Chemical	ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE Mass: 491.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1357 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.11 Å³/Da / Density % sol: 60.39 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 1.4M NaCl, 8% (w/vol) PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979183 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979183 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 118973 / % possible obs: 98.7 % / Redundancy: 8.9 % / B_iso Wilson estimate: 37.21 Å² / R_merge(I) obs: 0.083 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 7.9 % / R_merge(I) obs: 0.801 / Num. unique obs: 5892 / % possible all: 99

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1R1R

1r1r

Resolution: 2.1→49.15 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.192	3712	3.12 %
R_work	0.159	-	-
obs	0.16	118834	98.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 48.45 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→49.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11659	0	106	1357	13122

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 (%)
2.1-2.13	0.3091	124	0.2613	3872	X-RAY DIFFRACTION	91
2.13-2.15	0.2784	131	0.2457	4170	X-RAY DIFFRACTION	98
2.15-2.18	0.2575	138	0.2249	4256	X-RAY DIFFRACTION	99
2.18-2.22	0.2739	127	0.2198	4062	X-RAY DIFFRACTION	94
2.22-2.25	0.2523	137	0.2105	4241	X-RAY DIFFRACTION	99
2.25-2.28	0.2335	138	0.1996	4244	X-RAY DIFFRACTION	99
2.28-2.32	0.2614	138	0.1986	4287	X-RAY DIFFRACTION	99
2.32-2.36	0.2411	137	0.1939	4215	X-RAY DIFFRACTION	100
2.36-2.4	0.2251	138	0.1891	4278	X-RAY DIFFRACTION	99
2.4-2.45	0.2261	137	0.1849	4258	X-RAY DIFFRACTION	99
2.45-2.5	0.2579	138	0.1932	4257	X-RAY DIFFRACTION	100
2.5-2.55	0.2214	139	0.1825	4255	X-RAY DIFFRACTION	99
2.55-2.61	0.2528	138	0.175	4299	X-RAY DIFFRACTION	99
2.61-2.68	0.2182	137	0.1783	4159	X-RAY DIFFRACTION	97
2.68-2.75	0.203	136	0.1746	4207	X-RAY DIFFRACTION	98
2.75-2.83	0.2258	139	0.1713	4288	X-RAY DIFFRACTION	100
2.83-2.92	0.2375	138	0.1767	4308	X-RAY DIFFRACTION	99
2.92-3.03	0.2322	141	0.1776	4311	X-RAY DIFFRACTION	99
3.03-3.15	0.2123	139	0.1864	4310	X-RAY DIFFRACTION	99
3.15-3.29	0.1998	140	0.1615	4315	X-RAY DIFFRACTION	100
3.29-3.47	0.2073	135	0.1494	4295	X-RAY DIFFRACTION	99
3.47-3.68	0.1479	134	0.1383	4217	X-RAY DIFFRACTION	96
3.68-3.97	0.1467	143	0.1269	4376	X-RAY DIFFRACTION	100
3.97-4.37	0.1497	139	0.1205	4365	X-RAY DIFFRACTION	100
4.37-5	0.1457	143	0.1201	4402	X-RAY DIFFRACTION	100
5-6.29	0.1658	142	0.1473	4333	X-RAY DIFFRACTION	97
6.3-49.15	0.1697	146	0.1557	4542	X-RAY DIFFRACTION	98

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	4.3236	1.3405	-1.3654	1.8157	-0.979	1.8795	-0.0174	-0.3697	-0.3987	0.1787	-0.0571	-0.0609	0.0806	0.0656	0.0673	0.3168	0.019	-0.0146	0.3284	0.0475	0.229	-26.8849	30.6548	9.8595
2	1.0226	-0.04	0.3491	0.5491	-0.0345	3.0544	0.004	0.1859	0.0976	-0.0491	0.0452	0.0027	0.1197	0.0703	-0.0549	0.1802	-0.0099	0.0144	0.2133	0.0295	0.2273	-23.9718	38.9057	-28.1769
3	1.3722	0.0361	0.1011	0.896	-0.0881	1.2367	0.0313	0.0889	0.2336	0.0625	0.0276	0.0805	-0.1326	-0.0873	-0.0532	0.2251	0.0159	0.0267	0.1941	0.0602	0.2761	-31.0808	50.7017	-21.5277
4	2.0887	0.8604	-0.131	2.25	-1.9749	2.0182	0.2348	3.062	0.8286	-2.3088	-0.0656	0.4989	0.0475	0.2784	-0.0178	1.0235	0.0097	0.0026	1.1942	0.13	0.6372	-24.7932	9.4359	-90.4259
5	2.862	1.4032	-2.7525	8.6997	2.6569	5.4443	0.3177	1.0062	-0.3055	-0.7537	-0.17	0.4409	0.3229	0.3117	-0.1503	0.4144	-0.0015	-0.0665	0.5704	-0.0697	0.3602	-29.4	1.6168	-84.0005
6	5.3051	3.2309	0.8887	4.5003	0.925	1.9993	-0.046	0.4298	0.7406	-0.338	-0.1132	0.4342	-0.326	-0.0597	0.1574	0.3611	0.0464	0.0114	0.5059	0.034	0.4223	-11.2363	17.3958	-74.9002
7	0.5744	-0.1373	-0.1942	0.876	0.2502	2.0551	-0.0099	-0.0356	-0.0126	0.1584	0.0143	-0.0819	0.0408	-0.1211	-0.0151	0.2563	-0.0247	-0.0284	0.2859	-0.0381	0.2645	-11.4915	10.402	-35.7103
8	1.4236	0.0584	0.0225	0.7864	0.2421	1.0851	-0.0073	0.0756	-0.0738	-0.0434	0.0712	-0.1438	0.0551	0.1341	-0.0612	0.2391	-0.0238	0.006	0.2457	-0.0903	0.2639	-0.596	2.5204	-48.6372
9	1.9422	0.0753	0.3486	0.9966	0.3351	4.8231	0.0918	0.1765	-0.2584	-0.0429	-0.0912	0.1509	0.2655	-0.5614	-0.0599	0.2867	-0.0581	0.0015	0.29	-0.1263	0.3624	-18.3105	-6.1595	-52.6913
10	4.2014	4.5164	5.6259	4.8965	6.0728	7.5494	-0.4964	-0.3931	2.2162	-0.363	-0.2703	1.83	-0.6509	-0.9296	0.7648	0.6951	0.1165	-0.0762	0.9995	0.1168	1.3108	-50.5134	54.1989	-38.756
11	4.335	2.1693	-4.8474	1.3957	-2.3854	5.5159	-0.3373	-0.4594	-2.416	0.5477	-0.171	0.3397	1.8138	-0.2729	0.5185	1.3462	-0.296	-0.018	0.9355	0.0523	1.0604	-18.962	-18.9288	-28.9446
12	7.3401	-3.5873	-2.8576	2.8702	2.2694	1.7946	-0.5453	-2.1802	-4.2328	1.0918	-0.1886	0.6033	3.8195	-1.6255	0.7587	1.5192	-0.2514	0.0483	0.8211	0.238	1.2748	-9.1675	-18.2686	-32.5858

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 5 THROUGH 168 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 169 THROUGH 371 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 372 THROUGH 737 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 20 THROUGH 29 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 30 THROUGH 46 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 58 THROUGH 188 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 189 THROUGH 390 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 391 THROUGH 624 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 625 THROUGH 737 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 1365 THROUGH 1375 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 1366 THROUGH 1370 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 1371 THROUGH 1375 )

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