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- PDB-8dda: Crystal structure of human aminoadipate semialdehyde synthase (AA... -

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Basic information

Entry
Database: PDB / ID: 8dda
TitleCrystal structure of human aminoadipate semialdehyde synthase (AASS), lysine ketoglutarate reductase (LKR) domain
ComponentsAlpha-aminoadipic semialdehyde synthase, mitochondrial
KeywordsOXIDOREDUCTASE
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 catabolism / lysine biosynthetic process via aminoadipic acid ...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 catabolism / lysine biosynthetic process via aminoadipic acid / transcription corepressor activity / histone binding / mitochondrial matrix / intracellular membrane-bounded organelle / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytosol / cytoplasm
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: 2.4 Å
AuthorsMuniz, J.R.C. / Kopec, J. / Rembeza, E. / Burgess-Brown, N. / Bountra, C. / Yue, W.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of human aminoadipate semialdehyde synthase (AASS), lysine ketoglutarate reductase (LKR) domain
Authors: Muniz, J.R.C. / Kopec, J. / Rembeza, E. / Burgess-Brown, N. / Bountra, C. / Yue, W.W.
History
DepositionJun 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

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Assembly

Deposited unit
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial
C: Alpha-aminoadipic semialdehyde synthase, mitochondrial
D: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,7476
Polymers212,5554
Non-polymers1922
Water4,774265
1
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
C: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3743
Polymers106,2772
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-23 kcal/mol
Surface area32880 Å2
MethodPISA
2
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial
D: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3743
Polymers106,2772
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-22 kcal/mol
Surface area32730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.045, 80.533, 91.508
Angle α, β, γ (deg.)77.160, 67.635, 79.425
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 53138.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Lysine-ketoglutarate reductase (LKR) domain, residues 1-476
Source: (gene. exp.) Homo sapiens (human) / Gene: AASS / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UDR5, saccharopine dehydrogenase (NADP+, L-lysine-forming), saccharopine dehydrogenase (NAD+, L-glutamate-forming)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350 -- 10% ethylene glycol -- 0.2M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.4→78.04 Å / Num. obs: 71194 / % possible obs: 90 % / Observed criterion σ(I): 1.2 / Redundancy: 2.4 % / CC1/2: 0.553 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.069 / Rrim(I) all: 0.098 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4508 / CC1/2: 0.553 / Rpim(I) all: 0.898 / Rrim(I) all: 1.269 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q99

2q99


Resolution: 2.4→78.04 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.638 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.284
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.258 3439 4.852 %
Rwork0.2184 67434 -
all0.22 --
obs-70873 89.614 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.811 Å2
Baniso -1Baniso -2Baniso -3
1--0.209 Å2-0.317 Å2-0.745 Å2
2---0.959 Å20.253 Å2
3---0.429 Å2
Refinement stepCycle: LAST / Resolution: 2.4→78.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12484 0 10 265 12759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01312786
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511968
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.64117365
X-RAY DIFFRACTIONr_angle_other_deg1.171.57427566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75251599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70521.963657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.201152104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6131584
X-RAY DIFFRACTIONr_chiral_restr0.0620.21699
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022838
X-RAY DIFFRACTIONr_nbd_refined0.1910.22222
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.210585
X-RAY DIFFRACTIONr_nbtor_refined0.150.25904
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.25464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2280
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.28
X-RAY DIFFRACTIONr_nbd_other0.1350.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.214
X-RAY DIFFRACTIONr_mcbond_it2.1054.556420
X-RAY DIFFRACTIONr_mcbond_other2.1054.556419
X-RAY DIFFRACTIONr_mcangle_it3.5466.8128005
X-RAY DIFFRACTIONr_mcangle_other3.5466.8138006
X-RAY DIFFRACTIONr_scbond_it1.8154.7126366
X-RAY DIFFRACTIONr_scbond_other1.7524.7096359
X-RAY DIFFRACTIONr_scangle_it2.9897.0089358
X-RAY DIFFRACTIONr_scangle_other2.987.0049347
X-RAY DIFFRACTIONr_lrange_it5.65652.2213192
X-RAY DIFFRACTIONr_lrange_other5.64452.20113164
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.0511747
X-RAY DIFFRACTIONr_ncsr_local_group_20.0910.0511600
X-RAY DIFFRACTIONr_ncsr_local_group_30.0860.0511798
X-RAY DIFFRACTIONr_ncsr_local_group_40.10.0511532
X-RAY DIFFRACTIONr_ncsr_local_group_50.0850.0511703
X-RAY DIFFRACTIONr_ncsr_local_group_60.0940.0511472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3272560.3175106X-RAY DIFFRACTION91.6581
2.462-2.530.3022460.314934X-RAY DIFFRACTION90.7021
2.53-2.6030.3422540.34670X-RAY DIFFRACTION88.9612
2.603-2.6830.3222160.2864280X-RAY DIFFRACTION83.0593
2.683-2.7710.2832630.2484611X-RAY DIFFRACTION94.0927
2.771-2.8680.2872340.2394484X-RAY DIFFRACTION93.5925
2.868-2.9760.2832010.2224344X-RAY DIFFRACTION93.1543
2.976-3.0980.2782470.2284079X-RAY DIFFRACTION92.0817
3.098-3.2350.271940.2223896X-RAY DIFFRACTION91.4989
3.235-3.3930.2491910.223688X-RAY DIFFRACTION89.5429
3.393-3.5760.271510.2323270X-RAY DIFFRACTION84.2818
3.576-3.7920.3391520.3192932X-RAY DIFFRACTION79.546
3.792-4.0540.2351560.1963159X-RAY DIFFRACTION91.1215
4.054-4.3780.2081400.1692928X-RAY DIFFRACTION91.0926
4.378-4.7940.191260.1522618X-RAY DIFFRACTION88.1465
4.794-5.3580.21110.1622279X-RAY DIFFRACTION84.0366
5.358-6.1820.2861070.192191X-RAY DIFFRACTION94.0262
6.182-7.5610.233790.1881853X-RAY DIFFRACTION91.6074
7.561-10.650.201800.1811281X-RAY DIFFRACTION84.2724
10.65-78.040.252350.224830X-RAY DIFFRACTION95.0549
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)
11.35070.08-0.15650.15720.02350.57660.0139-0.27050.18940.074-0.0023-0.1747-0.00730.0039-0.01160.0824-0.044-0.10290.1088-0.04210.261796.85949.21750.992
21.44620.33680.14260.4572-0.02540.7954-0.12940.2536-0.2659-0.20020.1423-0.17620.0852-0.1641-0.0130.1568-0.0832-0.00870.1125-0.06740.198592.47395.48116.404
32.04270.48680.05420.2013-0.13830.2836-0.20220.480.402-0.07650.16540.08490.0628-0.05970.03680.0848-0.0648-0.09170.20240.09380.235271.17651.64824.197
40.68460.2890.22091.0692-0.04340.47460.143-0.0133-0.28320.4314-0.1445-0.39730.0846-0.11160.00150.2215-0.1011-0.20750.07040.05780.3185104.41791.82650.802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 430
2X-RAY DIFFRACTION2ALLB2 - 428
3X-RAY DIFFRACTION3ALLC2 - 427
4X-RAY DIFFRACTION4ALLD1 - 428

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