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- PDB-7tur: Joint X-ray/neutron structure of aspastate aminotransferase (AAT)... -

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Basic information

Entry
Database: PDB / ID: 7tur
TitleJoint X-ray/neutron structure of aspastate aminotransferase (AAT) in complex with pyridoxamine 5'-phosphate (PMP)
ComponentsAspartate aminotransferase, cytoplasmic
KeywordsTRANSFERASE / PLP-dependent enzyme / homodimer / aspartate aminotransferase
Function / homology
Function and homology information


Aspartate and asparagine metabolism / Malate-aspartate shuttle / glutamate catabolic process to aspartate / phosphatidylserine decarboxylase activity / : / cysteine transaminase / L-cysteine transaminase activity / aspartate biosynthetic process / aspartate catabolic process / glycerol biosynthetic process ...Aspartate and asparagine metabolism / Malate-aspartate shuttle / glutamate catabolic process to aspartate / phosphatidylserine decarboxylase activity / : / cysteine transaminase / L-cysteine transaminase activity / aspartate biosynthetic process / aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / fatty acid homeostasis / response to glucocorticoid / Notch signaling pathway / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
DEUTERATED WATER / Chem-PLA / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDrago, V.N. / Kovalevsky, A.Y. / Dajnowicz, S. / Mueser, T.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137008-01A1 United States
Citation
Journal: Chem Sci / Year: 2022
Title: An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction.
Authors: Drago, V.N. / Dajnowicz, S. / Parks, J.M. / Blakeley, M.P. / Keen, D.A. / Coquelle, N. / Weiss, K.L. / Gerlits, O. / Kovalevsky, A. / Mueser, T.C.
#1: Journal: Acta Cryst. / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: 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: Aspartate aminotransferase, cytoplasmic
B: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7904
Polymers93,1642
Non-polymers6262
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint4 kcal/mol
Surface area30320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.710, 125.030, 130.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aspartate aminotransferase, cytoplasmic / cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate ...cAspAT / Cysteine aminotransferase / cytoplasmic / Cysteine transaminase / cCAT / Glutamate oxaloacetate transaminase 1 / Transaminase A


Mass: 46581.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: GOT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00503, aspartate transaminase, cysteine transaminase
#2: Chemical ChemComp-PLA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID / N-PYRIDOXYL-2-METHYLASPARTIC ACID-5-MONOPHOSPHATE


Mass: 378.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 7.5
Details: 40 mM NaOAc (pH 5.4), 2 mM PLP, 9% polyethylene glycol (PEG) 6000, and 10% glycerol. The crystal soaked with 50 mM Tris-HCl (pH 7.5), 5% PEG 6000, 5% glycerol, and 300 mM L-cysteinesulfinate in D2O for 24 h

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A11
NUCLEAR REACTORILL LADI III23.10-4.15
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 12M1PIXELNov 15, 2018MIRRORS
MAATEL IMAGINE2IMAGE PLATEOct 4, 2018COLLIMATORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2NONELAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
23.11
34.151
Reflection

Entry-ID: 7TUR

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.7-47.39655695.330.039118.3
2.2-55.2133902755.40.16127.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
1.7-1.762.20.373.39507196.5
2.2-2.324.30.3084.44048261.6

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Processing

Software
NameVersionClassificationNB
nCNS1.0.0refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
LAUEGENdata reduction
LSCALEdata scaling
nCNSphasing
Refinement

Biso max: 112.5 Å2 / Biso mean: 29.37 Å2 / Biso min: 6.87 Å2 / % reflection Rfree: 5 % / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used

Starting modelResolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)Bsol (Å2)ksol (e/Å3)
5VJZ

5vjz

1.7-39.71X-RAY DIFFRACTION0.2330.0040.2034298874971012788575486.447.46730.303141
2.22-39.71NEUTRON DIFFRACTION0.2650.0070.237153231861460153186167.440.5050.532654
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.220.19
Luzzati d res low-5
Luzzati sigma a0.180.17
Luzzati d res high-1.7
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.380.33
Luzzati d res low-5
Luzzati sigma a0.560.49
Luzzati d res high-2.22
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 1.7→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 41 376 6977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg25.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.77
NEUTRON DIFFRACTIONx_bond_d0.01
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg25.9
NEUTRON DIFFRACTIONx_torsion_impr_deg0.77
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.7-1.780.3413534.80.3296949X-RAY DIFFRACTION0.01812511730258.4
1.78-1.870.26646950.2488987X-RAY DIFFRACTION0.01212563945675.3
1.87-1.990.25252850.229943X-RAY DIFFRACTION0.011125901047183.2
1.99-2.140.22855550.21210537X-RAY DIFFRACTION0.01125601109288.3
2.14-2.360.24257650.20910905X-RAY DIFFRACTION0.01126041148191.1
2.36-2.70.24358650.21311167X-RAY DIFFRACTION0.01126531175392.9
2.7-3.40.23560050.20611399X-RAY DIFFRACTION0.01127461199994.1
3.4-39.710.20561250.17511588X-RAY DIFFRACTION0.008131841220092.5
2.22-2.320.35714750.3632793NEUTRON DIFFRACTION0.0295700294051.6
2.32-2.440.3831434.60.3522977NEUTRON DIFFRACTION0.0325679312054.9
2.44-2.60.35516050.3213057NEUTRON DIFFRACTION0.0285651321756.9
2.6-2.80.3561634.70.3113314NEUTRON DIFFRACTION0.0285728347760.7
2.8-3.080.3441884.80.2813714NEUTRON DIFFRACTION0.0255717390268.3
3.08-3.520.222204.90.2124233NEUTRON DIFFRACTION0.0155738445377.6
3.52-4.440.1762444.70.1514907NEUTRON DIFFRACTION0.0115799515188.8
4.44-39.710.1942674.80.1675334NEUTRON DIFFRACTION0.0126048560192.6

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