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- PDB-4kxk: Alanine-glyoxylate aminotransferase variant K390A/K391A in comple... -

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Basic information

Entry
Database: PDB / ID: 4kxk
TitleAlanine-glyoxylate aminotransferase variant K390A/K391A in complex with the TPR domain of human Pex5p
Components
  • Peroxisomal targeting signal 1 receptor
  • Serine--pyruvate aminotransferase
KeywordsTRANSFERASE/TRANSPORT PROTEIN / TPR-domain / aminotransferase / pyruvate / transport / peroxisomal import / primary hyperoxaluria / Peroxisome / TRANSFERASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / oxalic acid secretion / serine-pyruvate transaminase / protein targeting to peroxisome / alanine-glyoxylate transaminase / peroxisome matrix targeting signal-1 binding ...protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / oxalic acid secretion / serine-pyruvate transaminase / protein targeting to peroxisome / alanine-glyoxylate transaminase / peroxisome matrix targeting signal-1 binding / glyoxylate metabolic process / glycine biosynthetic process, by transamination of glyoxylate / L-alanine catabolic process / serine-pyruvate transaminase activity / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix / protein import into peroxisome matrix, docking / protein carrier chaperone / very long-chain fatty acid metabolic process / alanine-glyoxylate transaminase activity / cerebral cortex neuron differentiation / cell development / L-serine metabolic process / pexophagy / L-cysteine catabolic process / positive regulation of multicellular organism growth / Glyoxylate metabolism and glycine degradation / glyoxylate catabolic process / endoplasmic reticulum organization / mitochondrial membrane organization / peroxisomal membrane / transaminase activity / neuromuscular process / amino acid binding / fatty acid beta-oxidation / cerebral cortex cell migration / peroxisomal matrix / negative regulation of protein-containing complex assembly / Notch signaling pathway / Pexophagy / Peroxisomal protein import / protein tetramerization / neuron migration / small GTPase binding / cellular response to reactive oxygen species / peroxisome / : / pyridoxal phosphate binding / E3 ubiquitin ligases ubiquitinate target proteins / intracellular membrane-bounded organelle / Golgi apparatus / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
PEX5/PEX5L / Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. ...PEX5/PEX5L / Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Aspartate Aminotransferase, domain 1 / Tetratricopeptide repeats / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Tetratricopeptide repeat / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Alanine--glyoxylate aminotransferase / Peroxisomal targeting signal 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFodor, K. / Lou, Y. / Wilmanns, M.
CitationJournal: Traffic / Year: 2015
Title: Ligand-Induced Compaction of the PEX5 Receptor-Binding Cavity Impacts Protein Import Efficiency into Peroxisomes.
Authors: Fodor, K. / Wolf, J. / Reglinski, K. / Passon, D.M. / Lou, Y. / Schliebs, W. / Erdmann, R. / Wilmanns, M.
History
DepositionMay 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine--pyruvate aminotransferase
C: Serine--pyruvate aminotransferase
B: Peroxisomal targeting signal 1 receptor
D: Peroxisomal targeting signal 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,6817
Polymers158,4114
Non-polymers2703
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-65 kcal/mol
Surface area50680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.593, 74.698, 91.209
Angle α, β, γ (deg.)87.85, 83.62, 89.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serine--pyruvate aminotransferase / SPT / Alanine--glyoxylate aminotransferase / AGT


Mass: 43074.762 Da / Num. of mol.: 2 / Mutation: K390A,K391A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGXT, AGT1, SPAT / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase
#2: Protein Peroxisomal targeting signal 1 receptor / PTS1 receptor / PTS1R / PTS1-BP / Peroxin-5 / Peroxisomal C-terminal targeting signal import ...PTS1 receptor / PTS1R / PTS1-BP / Peroxin-5 / Peroxisomal C-terminal targeting signal import receptor / Peroxisome receptor 1


Mass: 36130.664 Da / Num. of mol.: 2 / Fragment: TPR domain, UNP residues 315-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEX5, PXR1 / Plasmid: pETM20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P50542
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1 M Bis-Tris (pH 5.3), 0.10 M LiSO4, 12 % [w/w] PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.812 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2011
RadiationMonochromator: Horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 2.9→19.8 Å / Num. obs: 32399 / Redundancy: 2.2 % / Rmerge(I) obs: 0.134

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R9A

3r9a


Resolution: 2.9→19.8 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.879 / SU B: 15.546 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23764 1643 5.1 %RANDOM
Rwork0.18407 ---
obs0.18678 30756 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.79 Å2-0.73 Å2
2---1.23 Å21.34 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10458 0 14 40 10512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910721
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210317
X-RAY DIFFRACTIONr_angle_refined_deg1.391.97814552
X-RAY DIFFRACTIONr_angle_other_deg0.835323701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72151346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65423.891478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.104151802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4281578
X-RAY DIFFRACTIONr_chiral_restr0.0710.21628
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022430
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 129 -
Rwork0.256 2281 -
obs--96.67 %

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