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- PDB-3r9a: Human alanine-glyoxylate aminotransferase in complex with the TPR... -

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Basic information

Entry
Database: PDB / ID: 3r9a
TitleHuman alanine-glyoxylate aminotransferase in complex with the TPR domain of human PEX5P
Components
  • Peroxisomal targeting signal 1 receptor
  • Serine--pyruvate aminotransferase
KeywordsTRANSFERASE/TRANSPORT PROTEIN / TPR-DOMAIN / PROTEIN-PROTEIN COMPLEX / PEROXISOME / AMINOTRANSF PYRUVATE / TRANSFERASE / DISEASE MUTATION / MEMBRANE / PEROXISO BIOGENESIS DISORDER / PROTEIN TRANSPORT / TPR REPEAT / TRANSPO ZELLWEGER SYNDROME / TRANSFERASE-TRANSPORT PROTEIN COMPLEX / MITOCHONDRION / PYRIDOXAL PHOSPHATE
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 / cerebral cortex neuron differentiation / Glyoxylate metabolism and glycine degradation / 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 / 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 / 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 / cytosol / cytoplasm
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
Alanine--glyoxylate aminotransferase / Peroxisomal targeting signal 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFodor, K. / Wilmanns, M.
CitationJournal: Plos Biol. / Year: 2012
Title: Molecular requirements for peroxisomal targeting of alanine-glyoxylate aminotransferase as an essential determinant in primary hyperoxaluria type 1
Authors: Fodor, K. / Wolf, J. / Erdmann, R. / Schliebs, W. / Wilmanns, M.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 11, 2011ID: 3IMZ
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: Peroxisomal targeting signal 1 receptor
C: Serine--pyruvate aminotransferase
D: Peroxisomal targeting signal 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3095
Polymers159,0994
Non-polymers2091
Water14,970831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-60 kcal/mol
Surface area49950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.367, 99.156, 127.698
Angle α, β, γ (deg.)90.00, 96.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43419.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGT1, AGXT, 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
#3: 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.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1M BIS-TRIS (PH5.3), 0.15M LISO4, 17% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 27, 2007
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.35→78.09 Å / Num. all: 61302 / Num. obs: 61118 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.115
Reflection shellResolution: 2.35→2.48 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→78.09 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / SU B: 18.268 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.425 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23917 3096 5.1 %RANDOM
Rwork0.18381 ---
obs0.18665 57997 99.65 %-
all-58201 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.797 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-1.12 Å2
2--2.44 Å2-0 Å2
3----3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.35→78.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10542 0 14 831 11387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210833
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.98314714
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.01951359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46923.828478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.599151818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3221579
X-RAY DIFFRACTIONr_chiral_restr0.0730.21643
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218227
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3561.56773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.695210846
X-RAY DIFFRACTIONr_scbond_it1.14534060
X-RAY DIFFRACTIONr_scangle_it1.9584.53864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 220 -
Rwork0.288 4089 -
obs--95.31 %
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)
10.5635-0.2060.05850.2871-0.07541.60040.0223-0.01830.06790.00410.01610.00640.0715-0.067-0.03840.0778-0.0141-0.02290.0061-0.00410.1045-9.8122-4.0171-4.6888
21.02140.34680.13740.78270.01460.74910.0907-0.02730.0006-0.0054-0.05290.02170.02280.0226-0.03780.07440.0390.00170.05780.02210.051214.4573-1.688234.6946
30.5250.14550.09360.28940.18631.59280.01150.10720.0469-0.0190.0481-0.01320.10110.4299-0.05960.02590.0118-0.00310.15920.00580.04616.036-6.0819-29.6372
40.9072-0.5530.09321.4609-0.15331.31680.0352-0.10420.01050.0312-0.0179-0.07330.0288-0.0953-0.01730.0209-0.0525-0.01170.17440.02780.0089-17.6353-4.0847-65.0136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 392
2X-RAY DIFFRACTION2B325 - 639
3X-RAY DIFFRACTION3C4 - 392
4X-RAY DIFFRACTION4D324 - 639

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