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- PDB-6tlk: Structure of methylene-tetrahydromethanopterin dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 6tlk
TitleStructure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT
ComponentsBifunctional protein MdtA
KeywordsOXIDOREDUCTASE / One-carbon metabolism / Enzyme catalysis / Dehydrogenase / Conformational changes / Methylotrophy
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / methylenetetrahydrofolate dehydrogenase (NADP+) / methylenetetrahydrofolate dehydrogenase (NADP+) activity / formaldehyde catabolic process / one-carbon metabolic process / cytoplasm
Similarity search - Function
Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain / Methylene-tetrahydromethanopterin dehydrogenase, N-terminal / Methylene tetrahydromethanopterin dehydrogenase, NADP-binding domain / Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain superfamily / Methylene-tetrahydromethanopterin dehydrogenase, N-terminal / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Bifunctional protein MdtA
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWagner, T. / Huang, G. / Demmer, U. / Warkentin, E. / Ermler, U. / Shima, S.
Funding support Germany, China, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research FoundationIron sulfur for life SH87/1-1 Germany
Ministry of Education (China)China Scholarship Council China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.
Authors: Huang, G. / Wagner, T. / Demmer, U. / Warkentin, E. / Ermler, U. / Shima, S.
History
DepositionDec 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein MdtA
B: Bifunctional protein MdtA
C: Bifunctional protein MdtA
D: Bifunctional protein MdtA
E: Bifunctional protein MdtA
F: Bifunctional protein MdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,32535
Polymers189,0766
Non-polymers7,24829
Water37,7052093
1
A: Bifunctional protein MdtA
B: Bifunctional protein MdtA
C: Bifunctional protein MdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,71414
Polymers94,5383
Non-polymers4,17611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-28 kcal/mol
Surface area32470 Å2
MethodPISA
2
D: Bifunctional protein MdtA
E: Bifunctional protein MdtA
F: Bifunctional protein MdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,61121
Polymers94,5383
Non-polymers3,07318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-38 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.923, 149.267, 78.559
Angle α, β, γ (deg.)90.000, 93.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Bifunctional protein MdtA


Mass: 31512.734 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria)
Gene: mtdA, MexAM1_META1p1728 / Plasmid: pET-24b(+)
Details (production host): The synthesized DNA fragment was inserted into the expression vector pET-24b (+) at the NdeI and SalI restriction-enzyme digestion-sites
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P55818, Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor, methylenetetrahydrofolate dehydrogenase (NADP+)

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Non-polymers , 7 types, 2122 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-H4M / 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN


Mass: 788.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H45N6O16P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2093 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.14 % / Description: Thick plate.
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The protein at 25 mg/ml was in 25 mM tris(hydroxymethyl)aminomethane (Tris)/HCl buffer pH 7.5 containing 150 mM NaCl, 5% glycerol and 2 mM dithiothreitol, supplemented with 2.5 mM methenyl- ...Details: The protein at 25 mg/ml was in 25 mM tris(hydroxymethyl)aminomethane (Tris)/HCl buffer pH 7.5 containing 150 mM NaCl, 5% glycerol and 2 mM dithiothreitol, supplemented with 2.5 mM methenyl-H4MPT and 2 mM NADP. The crystallization solution was 20% w/v polyethylene glycol 3350 and 200 mM magnesium formate. The crystallization drop contained 0.7 ul of protein solution and 0.7 ul crystallization solution
PH range: / / Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97992 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97992 Å / Relative weight: 1
ReflectionResolution: 1.8→78.401 Å / Num. obs: 161189 / % possible obs: 98.9 % / Redundancy: 3 % / Biso Wilson estimate: 28.48 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.044 / Rrim(I) all: 0.08 / Rsym value: 0.066 / Net I/av σ(I): 10.5 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.8-1.931.0320.8236240.5430.691.2471.03299.5
1.9-2.0130.5111.5224230.3420.6180.51199.5
2.01-2.1530.3122.5209490.2090.3770.31299.5
2.15-2.3230.1894.1196120.1260.2280.18999.4
2.32-2.5530.1246.1180080.0830.150.12499.3
2.55-2.8530.07410.2162490.0490.0890.07499
2.85-3.2930.04217.3142490.0280.0510.04298.5
3.29-4.0230.02823.8119430.0180.0330.02897.7
4.02-5.6930.02227.291680.0150.0270.02296.6
5.69-43.3163.10.0227.149640.0130.0240.0294.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LU9

1lu9


Resolution: 1.8→26.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.201 7909 4.91 %RANDOM
Rwork0.166 ---
obs0.167 161135 98.8 %-
Displacement parametersBiso max: 136.77 Å2 / Biso mean: 36.17 Å2 / Biso min: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.0754 Å20 Å25.0536 Å2
2---0.6214 Å20 Å2
3----0.454 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.8→26.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12548 0 489 2093 15130
Biso mean--41.63 42.77 -
Num. residues----1729
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5875SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4192HARMONIC5
X-RAY DIFFRACTIONt_it26189HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1723SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28217SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d26189HARMONIC50.009
X-RAY DIFFRACTIONt_angle_deg47297HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion13.72
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2672 580 4.86 %
Rwork0.2288 11364 -
all0.2306 11944 -
obs--99.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.08220.86390.24890.8134-0.03970.3720.0135-0.0067-0.03970.0394-0.0519-0.0079-0.09320.00730.0383-0.0294-0.01890.0047-0.05640.0093-0.003-10.228417.709359.5854
21.2370.5301-0.78170.4241-0.04630.2669-0.0876-0.0079-0.04810.0152-0.0013-0.1026-0.0057-0.03260.0889-0.0757-0.0168-0.0470.01030.0382-0.0225-48.9332-5.643754.2022
30.2995-0.35260.62820.3938-0.62891.31310.00110.10170.173-0.03920.08180.0240.05570.035-0.0829-0.0918-0.0672-0.01010.00760.13060.0456-33.338521.415820.4543
40.6339-0.14130.31710.47170.22751.50210.0044-0.1438-0.12330.048-0.00430.04260.18780.021-0.0002-0.0307-0.01940.0145-0.03310.0627-0.0543-13.4285-23.997458.8399
51.09830.71450.26650.5536-0.14120.61960.03110.06870.0152-0.0880.08530.03770.1717-0.0772-0.11640.0284-0.0189-0.0535-0.04990.0143-0.0373-33.9984-27.108317.5657
60.44780.182-0.02860.4778-0.60630.9001-0.020.02440.05180.0476-0.06670.0103-0.08030.22020.0867-0.0177-0.042-0.01190.00570.0135-0.05621.8783-0.013423.0665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 456
2X-RAY DIFFRACTION2{ B|* }B2 - 456
3X-RAY DIFFRACTION3{ C|* }C2 - 456
4X-RAY DIFFRACTION4{ D|* }D2 - 456
5X-RAY DIFFRACTION5{ E|* }E2 - 456
6X-RAY DIFFRACTION6{ F|* }F2 - 456

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