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- PDB-1h0c: The crystal structure of human alanine:glyoxylate aminotransferase -

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Basic information

Entry
Database: PDB / ID: 1h0c
TitleThe crystal structure of human alanine:glyoxylate aminotransferase
ComponentsSERINE--GLYOXYLATE AMINOTRANSFERASE
KeywordsTRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / L-serine metabolic process / L-cysteine catabolic process ...oxalic acid secretion / serine-pyruvate transaminase / alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process / serine-pyruvate transaminase activity / L-alanine catabolic process / alanine-glyoxylate transaminase activity / L-serine metabolic process / L-cysteine catabolic process / glyoxylate catabolic process / Glyoxylate metabolism and glycine degradation / transaminase activity / amino acid binding / peroxisomal matrix / Notch signaling pathway / Peroxisomal protein import / peroxisome / : / pyridoxal phosphate binding / intracellular membrane-bounded organelle / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(AMINOOXY)ACETIC ACID / PYRIDOXAL-5'-PHOSPHATE / Alanine--glyoxylate aminotransferase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsZhang, X. / Danpure, C.J. / Roe, S.M. / Pearl, L.H.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of Alanine:Glyoxylate Aminotransferase and the Relationship between Genotype and Enzymatic Phenotype in Primary Hyperoxaluria Type 1.
Authors: Zhang, X. / Roe, S.M. / Roe, S.M. / Hou, Y. / Bartlam, M. / Rao, Z. / Pearl, L.H. / Danpure, C.J.
History
DepositionJun 17, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE--GLYOXYLATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9549
Polymers43,0631
Non-polymers8918
Water2,576143
1
A: SERINE--GLYOXYLATE AMINOTRANSFERASE
hetero molecules

A: SERINE--GLYOXYLATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,90718
Polymers86,1262
Non-polymers1,78216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12640 Å2
ΔGint-47.4 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.330, 90.330, 142.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

21A-2045-

HOH

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Components

#1: Protein SERINE--GLYOXYLATE AMINOTRANSFERASE / AGT / SPT / ALANINE--GLYOXYLATE AMINOTRANSFERASE


Mass: 43062.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LYSINE - PYRIDOXAL PHOSPHATE AT A 209 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: P21549, alanine-glyoxylate transaminase, serine-pyruvate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-AOA / (AMINOOXY)ACETIC ACID / Aminooxyacetic acid


Mass: 91.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTIVITY: L-SERINE + PYRUVATE = 3-HYDROXYPYRUVATE + L- ALANINE. ACTIVITY: L-ALANINE + GLYOXYLATE = ...ACTIVITY: L-SERINE + PYRUVATE = 3-HYDROXYPYRUVATE + L- ALANINE. ACTIVITY: L-ALANINE + GLYOXYLATE = PYRUVATE + GLYCINE.

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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: 2.39 Å3/Da / Density % sol: 58.1 %
Crystal growMethod: microbatch / pH: 7.5
Details: CRYSTALS WERE GROWN BY THE MICROBATCH METHOD. 1UL OF PROTEIN SOLUTION (15MG/ML ) WAS ADDED TO 1UL OF PRECIPITANT (2.5% (V/V) 2-PROPANOL, 10% PEG4K, 0.1M NAHEPES PH 7.5).
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.5 / Method: batch method / Details: Zhang, X., (2001) Acta Crystallogr., D57, 1936.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein11
210 %PEG400011
30.1 Msodium HEPES11pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 21044 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.9
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Num. obs: 21044 / % possible obs: 99.9 % / Num. measured all: 161988 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.58 Å / Rmerge(I) obs: 0.177

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.5→47.49 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2760167.23 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1016 4.9 %RANDOM
Rwork0.231 ---
obs0.231 20672 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.0505 Å2 / ksol: 0.378986 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1-8.42 Å20 Å20 Å2
2--8.42 Å20 Å2
3----16.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 57 143 3153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 173 5 %
Rwork0.304 3256 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3AOA_HEP_GOL.PARAOA_HEP_GOL.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Num. reflection obs: 20672 / Num. reflection Rfree: 2258 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

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