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- PDB-4kyo: Alanine-glyoxylate aminotransferase variant K390A in complex with... -

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Basic information

Entry
Database: PDB / ID: 4kyo
TitleAlanine-glyoxylate aminotransferase variant K390A 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 / protein targeting to peroxisome / oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glyoxylate metabolic process ...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 / protein targeting to peroxisome / oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glyoxylate metabolic process / peroxisome matrix targeting signal-1 binding / L-alanine catabolic process / glycine biosynthetic process, by transamination of glyoxylate / protein import into peroxisome matrix, receptor recycling / L-serine-pyruvate transaminase activity / protein import into peroxisome matrix / alanine-glyoxylate transaminase activity / protein import into peroxisome matrix, docking / very long-chain fatty acid metabolic process / Glyoxylate metabolism and glycine degradation / cerebral cortex neuron differentiation / protein carrier chaperone / cell development / glyoxylate catabolic process / L-serine metabolic process / L-cysteine catabolic process / pexophagy / positive regulation of multicellular organism growth / endoplasmic reticulum organization / peroxisomal membrane / transaminase activity / mitochondrial membrane organization / 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 / cellular response to reactive oxygen species / protein tetramerization / Peroxisomal protein import / small GTPase binding / neuron migration / pyridoxal phosphate binding / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / intracellular membrane-bounded organelle / enzyme binding / Golgi apparatus / 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. / Aspartate Aminotransferase, domain 1 / TPR repeat profile. / Aspartate Aminotransferase, domain 1 / Tetratricopeptide repeats / 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: 2.2 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 29, 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)160,07520
Polymers158,5274
Non-polymers1,54816
Water12,773709
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-64 kcal/mol
Surface area49620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.556, 74.830, 91.751
Angle α, β, γ (deg.)87.23, 83.41, 89.83
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 43132.863 Da / Num. of mol.: 2 / Mutation: K390A
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: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P50542

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Non-polymers , 4 types, 725 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1 M Bis-Tris (pH=5.3), 0.12 M LiSO4, 17% (w/w) PEG 3350, 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 22, 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: 2.2→51.03 Å / Num. obs: 73170 / Redundancy: 2.6 % / Rmerge(I) obs: 0.114

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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: 2.2→19.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.539 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21753 3747 5 %RANDOM
Rwork0.17526 ---
obs0.17738 71036 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.249 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.99 Å2-0.07 Å2
2---0.36 Å20.72 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10422 0 86 709 11217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910747
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210374
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.98314567
X-RAY DIFFRACTIONr_angle_other_deg0.846323835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55151348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35424.051474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.272151802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.351574
X-RAY DIFFRACTIONr_chiral_restr0.0850.21631
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022411
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 289 -
Rwork0.23 5142 -
obs--96.79 %

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