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- PDB-8e8t: Structure of the short LOR domain of human AASS -

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Basic information

Entry
Database: PDB / ID: 8e8t
TitleStructure of the short LOR domain of human AASS
ComponentsAlpha-aminoadipic semialdehyde synthase, mitochondrial
KeywordsOXIDOREDUCTASE / lysine metabolism / ketoglutarate / mitochondrial / reductase
Function / homology
Function and homology information


saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / lysine biosynthetic process via aminoadipic acid / Lysine catabolism ...saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / lysine biosynthetic process via aminoadipic acid / Lysine catabolism / transcription corepressor activity / histone binding / mitochondrial matrix / intracellular membrane-bounded organelle / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Alpha-aminoadipic semialdehyde synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsKhamrui, S. / Lazarus, M.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124838 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R21HD102745 United States
CitationJournal: Open Biology / Year: 2022
Title: Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1.
Authors: Leandro, J. / Khamrui, S. / Suebsuwong, C. / Chen, P.J. / Secor, C. / Dodatko, T. / Yu, C. / Sanchez, R. / DeVita, R.J. / Houten, S.M. / Lazarus, M.B.
History
DepositionAug 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)96,6942
Polymers96,6942
Non-polymers00
Water4,486249
1
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial

A: Alpha-aminoadipic semialdehyde synthase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)96,6942
Polymers96,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3720 Å2
ΔGint-8 kcal/mol
Surface area32450 Å2
2
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial

B: Alpha-aminoadipic semialdehyde synthase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)96,6942
Polymers96,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3590 Å2
ΔGint-7 kcal/mol
Surface area33420 Å2
Unit cell
Length a, b, c (Å)77.356, 154.715, 70.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alpha-aminoadipic semialdehyde synthase, mitochondrial / LKR/SDH


Mass: 48347.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AASS / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UDR5, saccharopine dehydrogenase (NADP+, L-lysine-forming), saccharopine dehydrogenase (NAD+, L-glutamate-forming)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M NaCl, 0.1M HEPES, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 26, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.18→42.91 Å / Num. obs: 43284 / % possible obs: 96.7 % / Redundancy: 3.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.11 / Rrim(I) all: 0.206 / Net I/σ(I): 4.4 / Num. measured all: 132605 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.18-2.252.91.0891095137570.3670.7241.319198
8.99-42.913.10.07919766450.9840.0520.09611.890.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QRJ

2qrj


Resolution: 2.18→42.91 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 2278 5.27 %
Rwork0.2136 40969 -
obs0.2152 43247 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.22 Å2 / Biso mean: 43.6696 Å2 / Biso min: 16.59 Å2
Refinement stepCycle: final / Resolution: 2.18→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 0 249 6575
Biso mean---38.18 -
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036464
X-RAY DIFFRACTIONf_angle_d0.568762
X-RAY DIFFRACTIONf_chiral_restr0.044979
X-RAY DIFFRACTIONf_plane_restr0.0041137
X-RAY DIFFRACTIONf_dihedral_angle_d15.0223898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1801-2.22750.34471370.3136256698
2.2275-2.27930.36071450.3011256996
2.2793-2.33630.31811660.2875250598
2.3363-2.39940.31151360.2691258098
2.3994-2.470.28091060.2595255296
2.47-2.54980.28761600.2547258398
2.5498-2.64090.29611680.2525258298
2.6409-2.74660.30791300.2382261898
2.7466-2.87160.23761510.2159256598
2.8716-3.02290.2411450.2236258198
3.0229-3.21230.26931320.2303260597
3.2123-3.46020.23531440.2141257097
3.4602-3.80820.22881340.1782251394
3.8082-4.35880.19441490.1724248092
4.3588-5.48980.20551480.1704248992
5.4898-42.910.20441270.1934261191
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)
13.59091.5736-1.36076.6198-3.42484.0140.26440.1569-0.30180.32760.1290.06210.2581-0.2172-0.22690.34880.0099-0.05280.2219-0.01170.379143.2245.83143.596
24.21162.3088-1.42737.60141.43232.41260.01290.9901-0.9897-0.70580.0909-0.29420.5314-0.26930.28810.6109-0.01380.04870.423-0.04920.488241.11559.97836.358
31.83380.87980.53252.36410.10291.11150.2488-0.233-0.45320.2025-0.149-0.43090.29690.0221-0.03680.3716-0.0209-0.03780.26260.03820.398644.1848.30549.359
43.7939-0.4686-1.64353.56971.02052.92810.31731.013-0.4951-1.1326-0.09080.2280.38390.0356-0.06480.51770.0325-0.01740.3978-0.08320.389738.94744.07434.88
53.65311.8253-3.72414.24895.43392-0.09981.2615-1.5662-1.1699-0.3631-0.34340.9257-0.31010.27020.6596-0.21440.22471.1642-0.32960.899237.89632.30631.334
64.5976-0.2326-0.30672.5797-0.12251.63380.26340.3381-0.117-0.1469-0.32590.6127-0.1366-0.3814-0.03890.3822-0.06510.00350.3258-0.04130.469624.66843.96941.9
70.76220.2542-0.1561.37180.04510.6047-0.0660.0516-0.00810.0080.07010.14990.0523-0.06650.050.2278-0.0405-0.01240.2093-0.01150.210426.61476.22348.872
85.4918-1.1572.30242.7993-1.02823.2240.0312-0.8882-0.22290.60440.17020.2369-0.2187-0.68940.06080.3552-0.0436-0.0040.35690.00660.2857.44979.73550.496
91.94531.37581.34011.57021.0281.25890.0107-0.0322-0.070.1292-0.06540.20770.2977-0.05840.060.2983-0.05820.02260.2901-0.0260.33096.73370.60941.622
102.4976-1.73542.84862.29590.11567.3840.3944-0.3654-0.94140.01360.18390.24160.58410.4588-0.0680.6502-0.06170.04130.5959-0.22940.65099.55657.13733.332
113.65881.7410.07846.1816-1.2473.8437-0.43551.1521-0.0209-1.02510.12210.0672-0.39640.42630.05340.3735-0.0994-0.01530.53320.00490.348711.94176.15928.997
125.04483.40762.61862.92052.75452.87520.40980.56490.2682-0.4936-0.39260.4355-0.9419-0.57050.09160.4067-0.0906-0.05010.3332-0.0320.369219.20891.69537.928
131.6023-0.14430.26091.1760.02520.795-0.02810.56-0.3735-0.11790.0959-0.08170.13620.12180.03440.3216-0.03080.00640.3403-0.05390.312624.38571.61433.468
143.697-4.2682-2.06195.7611.96017.8854-0.08730.71680.6041-0.78380.14820.634-0.3185-0.81140.03120.77270.0401-0.05880.95760.09540.48120.6479.83522.414
151.1086-0.45190.61552.43870.01770.5363-0.04060.0362-0.0906-0.19730.07640.12260.254-0.11840.01970.2567-0.06730.06550.2314-0.03260.218430.69860.49243.071
161.9075-1.269-0.0412.31310.39310.1650.19160.2888-1.01580.1545-0.22610.03710.6384-0.4672-0.04220.5083-0.10180.0180.31440.01830.65927.98233.64341.66
172.76410.4984-1.05824.123-0.09431.5177-0.06250.03070.0425-0.40240.17241.1012-0.0076-0.28910.00140.3246-0.0517-0.07650.27480.06240.49312.26170.74173.075
182.09751.0223-0.61133.8191-1.00830.3136-0.0811-0.13160.29660.28210.0071.18080.1317-0.3801-0.14110.17110.12680.09260.39910.0821.67573.72975.4878.41
192.58830.175-0.6253.15390.57062.76240.0528-0.86170.23070.4494-0.34550.68890.3423-0.43170.00690.4222-0.04830.09150.5083-0.03050.68628.36263.9586.17
209.0712-1.38591.90445.5841-0.31424.7240.0308-1.4374-0.62630.6699-0.57070.82850.407-0.55630.04520.8630.02060.26320.80540.0850.75774.69459.45894.014
212.993-0.4317-0.18963.60590.73783.4976-0.4933-0.1861-0.7360.6772-0.00380.87231.09260.39370.09810.52190.01830.22730.37550.1030.695414.24850.87280.013
222.1420.1583-0.48291.65450.01820.1038-0.0223-0.1655-0.05420.141-0.07070.0947-0.0112-0.0295-0.00650.3078-0.02050.0270.22470.00920.187839.08168.06475.31
232.20810.3429-0.44572.3996-0.21991.322-0.1299-0.0003-0.1651-0.02780.0476-0.13030.14950.04860.00870.2939-0.0118-0.02370.22210.0020.227146.63763.1469.75
243.99590.6908-0.00655.335-0.30671.93190.11640.1196-1.0114-0.22280.1405-0.85730.73070.7852-0.00680.57310.08470.00750.44970.04970.472654.63250.79471.676
252.13540.7072-0.18312.39030.16241.6651-0.3371-0.0165-0.95350.54980.1624-1.18810.8051-0.18870.11120.71830.032-0.05010.27190.04580.490146.83443.72676.581
264.89790.1258-2.33353.8278-0.58842.5299-0.18190.2097-0.9841-0.0053-0.02780.41681.2654-1.1751-0.03491.3913-0.31030.08120.63430.1270.751636.98534.27485.439
273.27470.5959-0.05062.6362-0.42081.641-0.0175-0.443-0.57210.06490.20820.21270.5946-0.01950.07010.5276-0.0554-0.05120.31040.12190.361445.22950.03882.577
286.16613.02160.77145.5510.93432.46580.0668-0.7201-0.46710.1593-0.14970.08660.3038-0.02150.04940.6655-0.0469-0.10040.52270.15260.551945.41649.44491.487
292.1547-0.1410.29012.5852-0.58381.6130.0497-0.71570.01620.6312-0.0510.07480.1528-0.02740.02690.5761-0.03660.02880.36490.00480.324845.30959.51986.473
303.438-0.21510.76922.7677-0.00912.5177-0.1487-0.85890.52790.61070.0229-0.4588-0.35470.2747-0.00190.5233-0.0657-0.0120.45340.00330.304441.52666.592.473
312.86030.25070.68452.2633-0.76660.85930.1018-0.0899-0.03050.0676-0.11940.27940.16880.01350.0170.3924-0.040.05540.2741-0.03490.242626.962.90477.242
320.93790.0079-0.55143.30191.27320.8398-0.8631-0.2562-0.54720.92030.00881.82220.9009-0.2757-0.11880.5624-0.08750.22970.35350.01071.31753.31150.79379.863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 24:31 )A24 - 31
2X-RAY DIFFRACTION2( CHAIN A AND RESID 32:36 )A32 - 36
3X-RAY DIFFRACTION3( CHAIN A AND RESID 37:92 )A37 - 92
4X-RAY DIFFRACTION4( CHAIN A AND RESID 93:110 )A93 - 110
5X-RAY DIFFRACTION5( CHAIN A AND RESID 130:130 )A130
6X-RAY DIFFRACTION6( CHAIN A AND RESID 131:144 )A131 - 144
7X-RAY DIFFRACTION7( CHAIN A AND RESID 145:240 )A145 - 240
8X-RAY DIFFRACTION8( CHAIN A AND RESID 241:250 )A241 - 250
9X-RAY DIFFRACTION9( CHAIN A AND RESID 251:312 )A251 - 312
10X-RAY DIFFRACTION10( CHAIN A AND RESID 313:316 )A313 - 316
11X-RAY DIFFRACTION11( CHAIN A AND RESID 318:330 )A318 - 330
12X-RAY DIFFRACTION12( CHAIN A AND RESID 341:348 )A341 - 348
13X-RAY DIFFRACTION13( CHAIN A AND RESID 349:379 )A349 - 379
14X-RAY DIFFRACTION14( CHAIN A AND RESID 380:384 )A380 - 384
15X-RAY DIFFRACTION15( CHAIN A AND RESID 385:428 )A385 - 428
16X-RAY DIFFRACTION16( CHAIN A AND RESID 429:450 )A429 - 450
17X-RAY DIFFRACTION17( CHAIN B AND RESID 24:78 )B24 - 78
18X-RAY DIFFRACTION18( CHAIN B AND RESID 79:83 )B79 - 83
19X-RAY DIFFRACTION19( CHAIN B AND RESID 84:122 )B84 - 122
20X-RAY DIFFRACTION20( CHAIN B AND RESID 123:130 )B123 - 130
21X-RAY DIFFRACTION21( CHAIN B AND RESID 131:144 )B131 - 144
22X-RAY DIFFRACTION22( CHAIN B AND RESID 145:195 )B145 - 195
23X-RAY DIFFRACTION23( CHAIN B AND RESID 196:240 )B196 - 240
24X-RAY DIFFRACTION24( CHAIN B AND RESID 241:253 )B241 - 253
25X-RAY DIFFRACTION25( CHAIN B AND RESID 254:284 )B254 - 284
26X-RAY DIFFRACTION26( CHAIN B AND RESID 285:292 )B285 - 292
27X-RAY DIFFRACTION27( CHAIN B AND RESID 293:313 )B293 - 313
28X-RAY DIFFRACTION28( CHAIN B AND RESID 314:330 )B314 - 330
29X-RAY DIFFRACTION29( CHAIN B AND RESID 341:369 )B341 - 369
30X-RAY DIFFRACTION30( CHAIN B AND RESID 370:388 )B370 - 388
31X-RAY DIFFRACTION31( CHAIN B AND RESID 389:425 )B389 - 425
32X-RAY DIFFRACTION32( CHAIN B AND RESID 426:450 )B426 - 450

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