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- PDB-4o9u: Mechanism of transhydrogenase coupling proton translocation and h... -

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Basic information

Entry
Database: PDB / ID: 4o9u
TitleMechanism of transhydrogenase coupling proton translocation and hydride transfer
Components
  • NAD(P) transhydrogenase subunit alpha 2
  • NAD(P) transhydrogenase subunit beta
  • NAD/NADP transhydrogenase alpha subunit 1
KeywordsMEMBRANE PROTEIN / Nicotinamide nucleotide transhydrogenase / Couples proton motive / Hydride transfer / Holo-transhydrogease from Thermus thermophilus assembled from subunits alpha1 / alpha2 / truncated beta / and domain III as a dimer / Respiratory proton pump enzyme forming cytosolic NADP(H) / Protons and NAD(H) / NADP(H) / Proton translocation and hydride transfer / Periplasmic membrane and cytosol
Function / homology
Function and homology information


proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / oxidoreductase activity / nucleotide binding / plasma membrane
Similarity search - Function
NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain ...NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / DHS-like NAD/FAD-binding domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / proton-translocating NAD(P)(+) transhydrogenase / proton-translocating NAD(P)(+) transhydrogenase / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.926 Å
AuthorsLeung, J.H. / Yamaguchi, M. / Moeller, A. / Schurig-Briccio, L.A. / Gennis, R.B. / Potter, C.S. / Carragher, B. / Stout, C.D.
CitationJournal: Science / Year: 2015
Title: Structural biology. Division of labor in transhydrogenase by alternating proton translocation and hydride transfer.
Authors: Leung, J.H. / Schurig-Briccio, L.A. / Yamaguchi, M. / Moeller, A. / Speir, J.A. / Gennis, R.B. / Stout, C.D.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P) transhydrogenase subunit alpha 2
B: NAD(P) transhydrogenase subunit beta
C: NAD(P) transhydrogenase subunit alpha 2
D: NAD(P) transhydrogenase subunit beta
E: NAD/NADP transhydrogenase alpha subunit 1
F: NAD/NADP transhydrogenase alpha subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,37410
Polymers198,5616
Non-polymers2,8144
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30840 Å2
ΔGint-274 kcal/mol
Surface area68100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.331, 160.590, 139.624
Angle α, β, γ (deg.)90.00, 128.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NAD(P) transhydrogenase subunit alpha 2


Mass: 10649.571 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1779 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GR9, EC: 1.6.1.2
#2: Protein NAD(P) transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta


Mass: 47371.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1778 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GS0, EC: 1.6.1.2
#3: Protein NAD/NADP transhydrogenase alpha subunit 1


Mass: 41258.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1780 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GR8
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide nucleotide transhydrogenase subunit beta / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / References: EC: 1.6.1.2
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

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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: 3.93 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50 mM MgCl2, 0.5 M trimethylamine N-oxide, 26% polyethylenglycol 400, 2% octyl glucoside, 0.1mM NADP, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 6.926→38.9 Å / Num. all: 5015 / Num. obs: 4922 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.926→38.9 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.858 / SU B: 331.29 / SU ML: 2.702 / Cross valid method: THROUGHOUT / ESU R Free: 3.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28372 228 4.6 %RANDOM
Rwork0.21271 ---
obs0.21598 4694 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 160.054 Å2
Baniso -1Baniso -2Baniso -3
1--21.34 Å2-0 Å2-9.66 Å2
2---16.37 Å20 Å2
3---23.52 Å2
Refinement stepCycle: LAST / Resolution: 6.926→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13434 0 184 0 13618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01913900
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.99918905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96451794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5223.424476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.273152288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1921579
X-RAY DIFFRACTIONr_chiral_restr0.0640.22246
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110135
X-RAY DIFFRACTIONr_mcbond_it5.08815.8577203
X-RAY DIFFRACTIONr_mcangle_it9.32123.7738988
X-RAY DIFFRACTIONr_scbond_it3.84816.2336697
X-RAY DIFFRACTIONr_long_range_B_refined23.16121097
LS refinement shellResolution: 6.926→7.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 17 -
Rwork0.296 298 -
obs--86.78 %

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