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- PDB-6mvu: Structure of a bacterial ALDH16 active site mutant C295A complexe... -

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Basic information

Entry
Database: PDB / ID: 6mvu
TitleStructure of a bacterial ALDH16 active site mutant C295A complexed with p-nitrophenylacetate
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / ALDH16 / NAD / ROSSMANN FOLD
Function / homologyAldehyde dehydrogenase / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 4-nitrophenyl acetate / Aldehyde dehydrogenase
Function and homology information
Biological speciesLoktanella sp. 3ANDIMAR09 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.488 Å
AuthorsTanner, J.J. / Liu, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM093123 United States
CitationJournal: J Mol Biol / Year: 2019
Title: Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer.
Authors: Li-Kai Liu / John J Tanner /
Abstract: The aldehyde dehydrogenase (ALDH) superfamily is a vast group of enzymes that catalyze the NAD-dependent oxidation of aldehydes to carboxylic acids. ALDH16 is perhaps the most enigmatic member of the ...The aldehyde dehydrogenase (ALDH) superfamily is a vast group of enzymes that catalyze the NAD-dependent oxidation of aldehydes to carboxylic acids. ALDH16 is perhaps the most enigmatic member of the superfamily, owing to its extra C-terminal domain of unknown function and the absence of the essential catalytic cysteine residue in certain non-bacterial ALDH16 sequences. Herein we report the first production of recombinant ALDH16, the first biochemical characterization of ALDH16, and the first crystal structure of ALDH16. Recombinant expression systems were generated for the bacterial ALDH16 from Loktanella sp. and human ALDH16A1. Four high-resolution crystal structures of Loktanella ALDH16 were determined. Loktanella ALDH16 is found to be a bona fide enzyme, exhibiting NAD-binding, ALDH activity, and esterase activity. In contrast, human ALDH16A1 apparently lacks measurable aldehyde oxidation activity, suggesting that it is a pseudoenzyme, consistent with the absence of the catalytic Cys in its sequence. The fold of ALDH16 comprises three domains: NAD-binding, catalytic, and C-terminal. The latter is unique to ALDH16 and features a Rossmann fold connected to a protruding β-flap. The tertiary structural interactions of the C-terminal domain mimic the quaternary structural interactions of the classic ALDH superfamily dimer, a phenomenon we call "trans-hierarchical structural similarity." ALDH16 forms a unique dimer in solution, which mimics the classic ALDH superfamily dimer-of-dimer tetramer. Small-angle X-ray scattering shows that human ALDH16A1 has the same dimeric structure and fold as Loktanella ALDH16. We suggest that the Loktanella ALDH16 structure may be considered to be the archetype of the ALDH16 family.
History
DepositionOct 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,90513
Polymers161,6862
Non-polymers1,21911
Water22,0501224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-128 kcal/mol
Surface area49020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.383, 119.623, 158.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldehyde dehydrogenase /


Mass: 80842.977 Da / Num. of mol.: 2 / Mutation: C295A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loktanella sp. 3ANDIMAR09 (bacteria) / Gene: AN189_10795 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q3EUQ3
#2: Chemical ChemComp-K4V / 4-nitrophenyl acetate / P-NITROPHENYL ACETATE


Mass: 181.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1224 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein was concentrated to 6 mg/ml in a storage buffer consisting of 20 mM Tris-HCl at pH 8.0, 100 mM NaCl, 2.5% glycerol and 0.5 mM TCEP. The crystallization reservoir solution contained ...Details: Protein was concentrated to 6 mg/ml in a storage buffer consisting of 20 mM Tris-HCl at pH 8.0, 100 mM NaCl, 2.5% glycerol and 0.5 mM TCEP. The crystallization reservoir solution contained 20% (w/v) polyethylene glycol (PEG) 3350, 200 mM ammonium sulfate and 100 mM Bis-Tris at pH 5.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.488→119.62 Å / Num. obs: 470410 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.055 / Rrim(I) all: 0.144 / Net I/σ(I): 8.8
Reflection shellResolution: 1.488→1.51 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.799 / Num. unique obs: 11001 / CC1/2: 0.44 / Rpim(I) all: 0.748 / Rrim(I) all: 1.952 / % possible all: 90.8

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model built with Swiss-Model using 5kf6 as the template

5kf6


Resolution: 1.488→95.519 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.94 / Phase error: 23.68
RfactorNum. reflection% reflection
Rfree0.2158 23461 4.99 %
Rwork0.1916 --
obs0.1928 470410 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.04 Å2 / Biso mean: 21.4238 Å2 / Biso min: 10.99 Å2
Refinement stepCycle: final / Resolution: 1.488→95.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11083 0 85 1231 12399
Biso mean--38.12 29.33 -
Num. residues----1504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4877-1.50460.35367180.3414130471376586
1.5046-1.52230.35437510.3261145811533296
1.5223-1.54090.34287900.3259147781556897
1.5409-1.56040.33447790.3123147931557298
1.5604-1.58090.33128200.301148201564098
1.5809-1.60260.32287200.2949149071562798
1.6026-1.62550.31187350.2904149201565598
1.6255-1.64980.29717740.287149771575198
1.6498-1.67550.29548060.275148361564298
1.6755-1.7030.28747810.2651149301571198
1.703-1.73240.26897740.2549149941576899
1.7324-1.76390.26318120.2437149101572298
1.7639-1.79780.26088010.2362149371573899
1.7978-1.83450.23817500.2294150741582499
1.8345-1.87440.24597800.2264150011578199
1.8744-1.9180.24047570.2083149581571599
1.918-1.9660.22277660.1934150831584999
1.966-2.01910.21637680.1868149501571898
2.0191-2.07860.21217900.1834150211581199
2.0786-2.14570.2187710.1747151151588699
2.1457-2.22240.20147730.1683150531582699
2.2224-2.31130.21197800.1699151321591299
2.3113-2.41650.20338260.16991499515821100
2.4165-2.5440.21448220.1761150041582699
2.544-2.70330.19657690.1695150821585199
2.7033-2.91210.19988030.17441511915922100
2.9121-3.20520.21018230.17441509615919100
3.2052-3.6690.18698560.1685149031575999
3.669-4.62250.15448190.1434149661578599
4.6225-95.71620.17917470.1661149671571498
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)
10.3375-0.05430.01020.1760.04990.2570.0227-0.0378-0.01420.00360.001-0.0106-0.00110.0199-0.02370.1573-0.0125-0.0020.144-0.00890.1289-36.32462.5394-10.5001
20.40280.022-0.00370.2009-0.02020.230.04180.05-0.0022-0.0056-0.01260.00220.0013-0.0115-0.0290.15370.01660.00140.14280.0060.1215-42.72223.1475-49.9276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and not (resname NPA))A0
2X-RAY DIFFRACTION2(chain 'B' and not (resname NPA))B0

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