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- PDB-9e15: Alpha-Delta heterodimeric form of soluble hydrogenase I from Pyro... -

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Basic information

Entry
Database: PDB / ID: 9.0E+15
TitleAlpha-Delta heterodimeric form of soluble hydrogenase I from Pyrococcus furiosus. Data processed and model refined in P1
Components(Sulfhydrogenase 1 subunit ...) x 2
KeywordsLYASE / Ni-Fe hydrogenase
Function / homology
Function and homology information


hydrogen dehydrogenase (NADP+) / hydrogen dehydrogenase (NADP+) activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
: / : / : / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit
Similarity search - Domain/homology
CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / PHOSPHATE ION / IRON/SULFUR CLUSTER / Sulfhydrogenase 1 subunit delta / Sulfhydrogenase 1 subunit alpha
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLanzilotta, W.N. / McTernan, P.M. / Adams, M.W.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural insights into the biotechnologically relevant reversible NADPH-oxidizing NiFe-hydrogenase from P.furiosus.
Authors: Xiansha Xiao / Gerrit J Schut / Xiang Feng / Patrick M McTernan / Dominik K Haja / William N Lanzilotta / Michael W W Adams / Huilin Li /
Abstract: The cytoplasmic hydrogenase I (SHI) from the hyperthermophilic archaeon Pyrococcus furiosus belongs to the group III hydrogenase family. SHI oxidizes NADPH rather than NADH to reduce protons and ...The cytoplasmic hydrogenase I (SHI) from the hyperthermophilic archaeon Pyrococcus furiosus belongs to the group III hydrogenase family. SHI oxidizes NADPH rather than NADH to reduce protons and evolve hydrogen gas, and because of this property, coupled with its high thermal stability, the enzyme holds great potential for economical hydrogen production. Despite decades of efforts, the SHI structure has remained unknown. Here, we report the cryoelectron microscopic (cryo-EM) structures of the heterotetrameric SHI holoenzyme (αδβγ). SHI is a symmetric dimer of two individually functional heterotetramers. SHI-αδ resembles the standard [NiFe] hydrogenase, and SHI-βγ function as the NADPH oxidoreductase. SHI-β contains three [4Fe-4S] clusters that relay electrons from NADPH in SHI-γ to the catalytic [NiFe] cluster in SHI-αδ for H production. These structures will guide the adaptation of this unique enzyme for biotechnological applications.
History
DepositionOct 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfhydrogenase 1 subunit delta
B: Sulfhydrogenase 1 subunit alpha
C: Sulfhydrogenase 1 subunit delta
D: Sulfhydrogenase 1 subunit alpha
E: Sulfhydrogenase 1 subunit delta
F: Sulfhydrogenase 1 subunit alpha
G: Sulfhydrogenase 1 subunit delta
H: Sulfhydrogenase 1 subunit alpha
I: Sulfhydrogenase 1 subunit delta
J: Sulfhydrogenase 1 subunit alpha
K: Sulfhydrogenase 1 subunit delta
L: Sulfhydrogenase 1 subunit alpha
M: Sulfhydrogenase 1 subunit delta
N: Sulfhydrogenase 1 subunit alpha
O: Sulfhydrogenase 1 subunit delta
P: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)635,52469
Polymers624,43416
Non-polymers11,08953
Water6,666370
1
A: Sulfhydrogenase 1 subunit delta
B: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4949
Polymers78,0542
Non-polymers1,4397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-110 kcal/mol
Surface area24440 Å2
MethodPISA
2
C: Sulfhydrogenase 1 subunit delta
D: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3047
Polymers78,0542
Non-polymers1,2505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-110 kcal/mol
Surface area24270 Å2
MethodPISA
3
E: Sulfhydrogenase 1 subunit delta
F: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4949
Polymers78,0542
Non-polymers1,4397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-123 kcal/mol
Surface area24660 Å2
MethodPISA
4
G: Sulfhydrogenase 1 subunit delta
H: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4239
Polymers78,0542
Non-polymers1,3697
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-112 kcal/mol
Surface area24450 Å2
MethodPISA
5
I: Sulfhydrogenase 1 subunit delta
J: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4949
Polymers78,0542
Non-polymers1,4397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-116 kcal/mol
Surface area24430 Å2
MethodPISA
6
K: Sulfhydrogenase 1 subunit delta
L: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3998
Polymers78,0542
Non-polymers1,3446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-107 kcal/mol
Surface area24910 Å2
MethodPISA
7
M: Sulfhydrogenase 1 subunit delta
N: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3047
Polymers78,0542
Non-polymers1,2505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-110 kcal/mol
Surface area24770 Å2
MethodPISA
8
O: Sulfhydrogenase 1 subunit delta
P: Sulfhydrogenase 1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,61311
Polymers78,0542
Non-polymers1,5599
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-123 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.235, 111.148, 141.091
Angle α, β, γ (deg.)90.06, 90.02, 90.00
Int Tables number1
Space group name H-MP1

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Components

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Sulfhydrogenase 1 subunit ... , 2 types, 16 molecules ACEGIKMOBDFHJLNP

#1: Protein
Sulfhydrogenase 1 subunit delta / Hydrogenase I small subunit / NADP-reducing hydrogenase subunit HydD / Sulfhydrogenase I subunit delta


Mass: 30141.016 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: hydD, PF0893 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: E7FHU4, hydrogen dehydrogenase (NADP+)
#2: Protein
Sulfhydrogenase 1 subunit alpha / Hydrogenase I large subunit / NADP-reducing hydrogenase subunit HydA / Sulfhydrogenase I subunit alpha


Mass: 47913.262 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: hydA, PF0894 / Production host: Pyrococcus furiosus (archaea) / References: UniProt: E7FI44, hydrogen dehydrogenase (NADP+)

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Non-polymers , 6 types, 423 molecules

#3: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3FeN2O
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.5
Details: Capillary Batch method under atmosphere of 95% Nitrogen, 5% hydrogen; 50 mM potassium phosphate pH 7.5, 150 mM NaCl, 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.34 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Jan 15, 2018
RadiationMonochromator: 1.34 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 175212 / % possible obs: 99.3 % / Redundancy: 2 % / CC1/2: 0.971 / CC star: 0.993 / Net I/σ(I): 8.3
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 16453 / CC1/2: 0.48 / CC star: 0.806

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→35.84 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3055 2002 1.16 %
Rwork0.2669 --
obs0.2674 173078 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42910 0 57 370 43337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.835
X-RAY DIFFRACTIONf_dihedral_angle_d21.25716575
X-RAY DIFFRACTIONf_chiral_restr0.0696554
X-RAY DIFFRACTIONf_plane_restr0.0117587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.39431260.325410715X-RAY DIFFRACTION87
2.67-2.740.38861360.328912166X-RAY DIFFRACTION98
2.74-2.820.42491420.316912253X-RAY DIFFRACTION99
2.82-2.910.3621440.302412334X-RAY DIFFRACTION99
2.91-3.010.35711410.284712319X-RAY DIFFRACTION99
3.01-3.130.33451450.278212411X-RAY DIFFRACTION100
3.13-3.280.30811400.275912334X-RAY DIFFRACTION100
3.28-3.450.35811470.275412403X-RAY DIFFRACTION100
3.45-3.670.33121460.269612340X-RAY DIFFRACTION100
3.67-3.950.32811460.256412397X-RAY DIFFRACTION100
3.95-4.350.28521480.240612365X-RAY DIFFRACTION100
4.35-4.970.22131480.227712422X-RAY DIFFRACTION100
4.97-6.260.29641440.258412322X-RAY DIFFRACTION100
6-6.690.29451490.268312295X-RAY DIFFRACTION99

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