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- PDB-4a0r: Structure of bifunctional DAPA aminotransferase-DTB synthetase fr... -

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Basic information

Entry
Database: PDB / ID: 4a0r
TitleStructure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana bound to dethiobiotin (DTB).
ComponentsADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
KeywordsTRANSFERASE / BIO3-BIO1 / BIOTIN SYNTHESIS
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / dethiobiotin synthase / dethiobiotin synthase activity / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / magnesium ion binding / protein homodimerization activity / mitochondrion / ATP binding
Similarity search - Function
Dethiobiotin synthase BioD / AAA domain / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Dethiobiotin synthase BioD / AAA domain / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DTB / PYRIDOXAL-5'-PHOSPHATE / L(+)-TARTARIC ACID / Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsCobessi, D. / Dumas, R. / Pautre, V. / Meinguet, C. / Ferrer, J.L. / Alban, C.
CitationJournal: Plant Cell / Year: 2012
Title: Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin Synthetase-Diaminopelargonic Acid Aminotransferase: Evidence for Substrate Channeling in Biotin Synthesis.
Authors: Cobessi, D. / Dumas, R. / Pautre, V. / Meinguet, C. / Ferrer, J.L. / Alban, C.
History
DepositionSep 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Other / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
B: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,0778
Polymers182,8542
Non-polymers1,2236
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17460 Å2
ΔGint-100 kcal/mol
Surface area48600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)246.670, 76.630, 79.840
Angle α, β, γ (deg.)90.00, 108.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 9:41 OR RESSEQ 48:100 OR RESSEQ...
211CHAIN B AND (RESSEQ 9:41 OR RESSEQ 48:100 OR RESSEQ...

NCS oper: (Code: given
Matrix: (0.730856, -0.116748, -0.672472), (-0.113581, -0.992328, 0.048836), (-0.673015, 0.040688, -0.738509)
Vector: 17.19159, 2.92256, 43.99862)

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Components

#1: Protein ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE / ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE/DETHIOBIOTIN SYNTHETASE / MITOCHONDRIAL ...ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE/DETHIOBIOTIN SYNTHETASE / MITOCHONDRIAL BIFUNCTIONAL DIAMINOPELARGONATE SYNTHASE- DETHIOBIOTIN SYNTHETASE / DETHIOBIOTIN SYNTHETASE-DIAMINOPELARGONIC ACID AMINOTRANSFERASE


Mass: 91427.188 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-833
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2
References: UniProt: B0F481, dethiobiotin synthase, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-DTB / 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID / D-DESTHIOBIOTIN


Mass: 214.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.91 Å3/Da / Density % sol: 35.8 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM TARTRATE PH 6.2, 15 % PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.68→40.44 Å / Num. obs: 40026 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 34.68 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.95
Reflection shellResolution: 2.68→2.75 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.83 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE DETHIOBIOTIN SYNTHETASE- DIAMINOPELARGONIC ACID AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA

Resolution: 2.68→40.436 Å / SU ML: 0.79 / σ(F): 0 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 2006 5 %
Rwork0.1844 --
obs0.1881 40012 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.886 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.9779 Å20 Å2-3.018 Å2
2--3.5817 Å20 Å2
3----0.6038 Å2
Refinement stepCycle: LAST / Resolution: 2.68→40.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11470 0 80 121 11671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911838
X-RAY DIFFRACTIONf_angle_d1.25316106
X-RAY DIFFRACTIONf_dihedral_angle_d15.2324208
X-RAY DIFFRACTIONf_chiral_restr0.0771852
X-RAY DIFFRACTIONf_plane_restr0.0062052
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4885X-RAY DIFFRACTIONPOSITIONAL
12B4885X-RAY DIFFRACTIONPOSITIONAL0.161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6797-2.74670.33241430.24542713X-RAY DIFFRACTION100
2.7467-2.82090.32981380.23042682X-RAY DIFFRACTION100
2.8209-2.90390.32261280.22212712X-RAY DIFFRACTION100
2.9039-2.99760.31911500.21082689X-RAY DIFFRACTION100
2.9976-3.10470.30621350.20352704X-RAY DIFFRACTION100
3.1047-3.2290.27081410.18962688X-RAY DIFFRACTION100
3.229-3.37590.28911400.18072700X-RAY DIFFRACTION100
3.3759-3.55370.26551600.18732686X-RAY DIFFRACTION100
3.5537-3.77620.26261430.18462725X-RAY DIFFRACTION100
3.7762-4.06750.26811460.17422717X-RAY DIFFRACTION100
4.0675-4.47640.22541340.16032733X-RAY DIFFRACTION100
4.4764-5.12310.19451360.14582723X-RAY DIFFRACTION100
5.1231-6.45030.23461490.17992748X-RAY DIFFRACTION100
6.4503-40.4410.2221630.18732786X-RAY DIFFRACTION99
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)
11.41610.35570.44771.0097-0.04651.43260.0093-0.0248-0.23110.05510.03980.00180.2926-0.1872-0.05290.2912-0.06860.04030.15880.02160.2231-2.061-21.97725.7568
21.26370.01230.07930.44270.13490.56140.08980.0618-0.1223-0.0347-0.0043-0.01040.1919-0.0014-0.08190.2298-0.0065-0.01740.12950.02810.11669.9774-12.153612.3172
31.1572-0.19910.38680.90290.02530.84710.04590.0862-0.12430.06110.0281-0.17680.2570.2485-0.06510.21360.0836-0.00750.2406-0.0230.167146.3297-8.938423.5105
40.8563-0.04310.03861.24760.59681.91930.05650.02610.1547-0.1298-0.01210.0016-0.2382-0.009-0.03250.16620.02290.03880.13050.02080.26570.515926.287126.7528
50.9416-0.332-0.46440.24050.13880.68780.0435-0.00790.16810.0116-0.0008-0.0263-0.11380.0533-0.03770.1617-0.0126-0.01690.133-0.00020.16716.617514.826827.1347
60.8570.2107-0.05551.0007-0.25591.1777-0.06610.24480.1607-0.1010.021-0.13-0.050.34470.03480.1585-0.0381-0.01910.3260.03990.173136.67267.4517-5.0676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 7:202)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 203:375)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 376:809)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 9:170)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 171:375)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 376:807)

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