PDB-8uy2: Methylenetetrahydrofolate reductase from Chaetomium thermophilum ...

ID or keywords:

Entry

Database: PDB / ID: 8uy2

Title

Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, AdoMet-bound, Inhibited (T) State

Components

Methylenetetrahydrofolate reductase-like protein

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / methylenetetrahydrofolate reductase / NADPH activity / oxidoreductase activity / acting on the CH-NH group of donors / NAD or NADP as acceptor cobalamin binding / one-carbon metabolism / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

Function / homology

Function and homology information

methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / cytosol
Similarity search - Function

Biological species

Thermochaetoides thermophila DSM 1495 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.83 Å

Authors

Yamada, K. / Mendoza, J. / Koutmos, M.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Structural basis of S-adenosylmethionine-dependent allosteric transition from active to inactive states in methylenetetrahydrofolate reductase.
Authors: Yamada, K. / Mendoza, J. / Koutmos, M.

History

Deposition	Nov 12, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8uy2.cif.gz	2 MB	Display	PDBx/mmCIF format
PDB format	pdb8uy2.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	8uy2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8uy2_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	8uy2_full_validation.pdf.gz	3.2 MB	Display
Data in XML	8uy2_validation.xml.gz	82 KB	Display
Data in CIF	8uy2_validation.cif.gz	111 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uy/8uy2 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/8uy2	HTTPS FTP

-
Related structure data

Related structure data	8uy1C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Methylenetetrahydrofolate reductase-like protein

B: Methylenetetrahydrofolate reductase-like protein

C: Methylenetetrahydrofolate reductase-like protein

D: Methylenetetrahydrofolate reductase-like protein

hetero molecules

289 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)	130.656, 149.948, 171.056
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 592
2	1	1	1	A	1 - 592
3	2	2	1	A	1 - 592
4	2	2	1	A	1 - 592
5	3	3	1	A	1 - 592
6	3	3	1	A	1 - 592
7	4	4	1	B	0 - 592
8	4	4	1	B	0 - 592
9	5	5	1	C	-2 - 593
10	5	5	1	C	-2 - 593
11	6	6	1	D	0 - 592
12	6	6	1	D	0 - 592

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Methylenetetrahydrofolate reductase-like protein Mass: 70256.531 Da / Num. of mol.: 4 / Mutation: R315A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0033700 / Production host: Escherichia coli (E. coli) References: UniProt: G0S5U9, methylenetetrahydrofolate reductase [NAD(P)H]

#1: Protein

Methylenetetrahydrofolate reductase-like protein

Mass: 70256.531 Da / Num. of mol.: 4 / Mutation: R315A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0033700 / Production host:

Escherichia coli (E. coli)
References: UniProt: G0S5U9, methylenetetrahydrofolate reductase [NAD(P)H]

-
Non-polymers , 7 types, 363 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.86 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 1-1 protein to reservoir solution, Protein: 50 mg/mL, 50 mM potassium phosphate buffer (KPB), pH 7.4, containing 500 uM AoMet and 250 uM FAD Reservoir Solution: 0.1 M sodium acetate, pH 4.8, ...Details: 1-1 protein to reservoir solution, Protein: 50 mg/mL, 50 mM potassium phosphate buffer (KPB), pH 7.4, containing 500 uM AoMet and 250 uM FAD Reservoir Solution: 0.1 M sodium acetate, pH 4.8, 0.2 M ammonium sulfate, 6% polyethylene glycol monomethyl ether 2,000

Crystal

Density Matthews: 2.99 Å³/Da / Density % sol: 58.86 %

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 1-1 protein to reservoir solution, Protein: 50 mg/mL, 50 mM potassium phosphate buffer (KPB), pH 7.4, containing 500 uM AoMet and 250 uM FAD Reservoir Solution: 0.1 M sodium acetate, pH 4.8, ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 1.1271 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2022

Radiation

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

Radiation wavelength

Wavelength: 1.1271 Å / Relative weight: 1

Reflection

Resolution: 2.83→75.087 Å / Num. obs: 80491 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC_1/2: 0.987 / R_merge(I) obs: 0.126 / R_pim(I) all: 0.077 / R_rim(I) all: 0.149 / Net I/σ(I): 10.1

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
14.43-74.97	5.5	0.076	705	0.972	0.048	0.091
2.83-2.89	7.2	1.171	4556	0.672	0.724	1.383

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
Aimless		data scaling
DIALS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.83→74.974 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.942 / WR_factor R_free: 0.198 / WR_factor R_work: 0.188 / SU B: 24.002 / SU ML: 0.219 / Average fsc free: 0.9692 / Average fsc work: 0.975 / Cross valid method: THROUGHOUT / ESU R: 1.779 / ESU R Free: 0.289
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2027	3970	4.939 %	RANDOM
R_work	0.1873	76411	-	-
all	0.188	-	-	-
obs	-	80381	99.603 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 75.216 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.655 Å²	0 Å²	0 Å²
2-	-	1.49 Å²	-0 Å²
3-	-	-	-0.835 Å²

Refinement step

Cycle: LAST / Resolution: 2.83→74.974 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17822	0	502	335	18659

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	18812
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.016	17256
X-RAY DIFFRACTION	r_angle_refined_deg	1.633	1.835	25567
X-RAY DIFFRACTION	r_angle_other_deg	1.37	1.776	39761
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.807	5	2213
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	20.794	5	137
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.724	10	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.838	10	3092
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.565	10	921
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	2691
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	22348
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	4388
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	3864
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.141	0.2	16550
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	9068
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.065	0.2	10385
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.108	0.2	412
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.196	0.2	65
X-RAY DIFFRACTION	r_nbd_other	0.117	0.2	154
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.092	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	4.894	5.098	8892
X-RAY DIFFRACTION	r_mcbond_other	4.892	5.098	8892
X-RAY DIFFRACTION	r_mcangle_it	7.466	9.177	11083
X-RAY DIFFRACTION	r_mcangle_other	7.465	9.178	11084
X-RAY DIFFRACTION	r_scbond_it	6.377	5.687	9920
X-RAY DIFFRACTION	r_scbond_other	6.341	5.673	9884
X-RAY DIFFRACTION	r_scangle_it	9.835	10.157	14482
X-RAY DIFFRACTION	r_scangle_other	9.79	10.133	14429
X-RAY DIFFRACTION	r_lrange_it	15.551	63.21	80793
X-RAY DIFFRACTION	r_lrange_other	15.554	63.199	80709
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.093	0.05	18301
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.091	0.05	18392
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.094	0.05	18299
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.093	0.05	18265
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.092	0.05	18460
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.101	0.05	18172

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09284	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09284	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09077	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.09077	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09432	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09432	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.09281	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.09281	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.09201	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.09201	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.10101	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.10101	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.83-2.903	0.319	289	0.287	5585	0.289	5879	0.935	0.949	99.9149	0.275
2.903-2.983	0.272	293	0.253	5439	0.254	5744	0.948	0.96	99.7911	0.233
2.983-3.069	0.255	272	0.238	5297	0.239	5574	0.962	0.965	99.9103	0.218
3.069-3.163	0.239	279	0.223	5173	0.224	5455	0.965	0.969	99.945	0.201
3.163-3.267	0.24	248	0.206	5023	0.208	5274	0.966	0.975	99.9431	0.185
3.267-3.381	0.212	241	0.188	4837	0.189	5080	0.972	0.979	99.9606	0.17
3.381-3.509	0.204	247	0.18	4689	0.181	4936	0.975	0.981	100	0.164
3.509-3.652	0.211	261	0.179	4473	0.181	4745	0.974	0.982	99.7682	0.165
3.652-3.814	0.198	213	0.175	4298	0.176	4561	0.976	0.982	98.9037	0.163
3.814-3.999	0.191	208	0.16	4079	0.161	4375	0.977	0.984	97.9886	0.151
3.999-4.215	0.16	204	0.145	3965	0.146	4172	0.984	0.987	99.9281	0.14
4.215-4.47	0.166	187	0.134	3739	0.135	3927	0.983	0.989	99.9745	0.134
4.47-4.777	0.175	181	0.149	3541	0.15	3723	0.982	0.987	99.9731	0.151
4.777-5.158	0.17	179	0.166	3296	0.166	3482	0.983	0.984	99.799	0.171
5.158-5.648	0.176	133	0.19	3062	0.189	3204	0.981	0.981	99.7191	0.193
5.648-6.31	0.238	133	0.203	2779	0.205	2931	0.969	0.978	99.3518	0.21
6.31-7.278	0.219	146	0.206	2418	0.207	2584	0.97	0.974	99.226	0.217
7.278-8.892	0.196	120	0.189	2059	0.189	2229	0.976	0.978	97.7568	0.212
8.892-12.488	0.151	93	0.174	1668	0.173	1762	0.987	0.984	99.9432	0.194
12.488-74.974	0.32	43	0.364	990	0.362	1057	0.94	0.921	97.7294	0.592

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	0.6103	0.0012	-0.6712	0.5618	-0.181	2.2162	-0.0393	0.0444	-0.0132	-0.0345	0.0103	0.2447	0.1615	-0.2048	0.0289	0.0439	-0.0252	-0.009	0.0231	-0.0057	0.1131	-3.2728	-32.6125	4.0336
2	0.5827	0.5826	-0.1949	2.0413	-0.5548	0.6079	0.0527	-0.077	-0.0543	0.4553	-0.0686	-0.0421	-0.1002	-0.0299	0.016	0.2074	0.02	0.0752	0.0243	0.0295	0.0699	7.5108	-4.7754	44.4212
3	0.737	-1.1175	-0.1111	2.2335	0.3035	0.645	-0.084	-0.0048	0.0452	0.3629	-0.105	-0.1606	0.0336	0.2251	0.1891	0.2002	0.0221	-0.0071	0.2279	0.2106	0.3583	58.7959	-17.4314	27.6574
4	0.608	-0.244	0.6278	0.9708	-0.4691	1.4191	0.129	0.0214	-0.2058	-0.168	-0.083	-0.0768	0.6013	0.1562	-0.046	0.3288	0.0998	0.1044	0.0374	0.0661	0.2519	47.4786	-42.4267	-14.2727

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 7 types, 363 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 7 types, 363 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 7 types, 363 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi