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- PDB-1akb: STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRA... -

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Basic information

Entry
Database: PDB / ID: 1akb
TitleSTRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRANSFERASE K258H LACKING ITS PYRIDOXAL-5'-PHOSPHATE-BINDING LYSINE RESIDUE
ComponentsASPARTATE AMINOTRANSFERASEAspartate transaminase
KeywordsTRANSFERASE(AMINOTRANSFERASE)
Function / homology
Function and homology information


Amino acid metabolism / Gluconeogenesis / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / aspartate catabolic process / 2-oxoglutarate metabolic process ...Amino acid metabolism / Gluconeogenesis / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / aspartate catabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / 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 / 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 ...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 / 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
Chem-PPD / Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMalashkevich, V.N. / Jansonius, J.N.
Citation
Journal: Biochemistry / Year: 1995
Title: Structural basis for the catalytic activity of aspartate aminotransferase K258H lacking the pyridoxal 5'-phosphate-binding lysine residue.
Authors: Malashkevich, V.N. / Jager, J. / Ziak, M. / Sauder, U. / Gehring, H. / Christen, P. / Jansonius, J.N.
#1: Journal: Eur.J.Biochem. / Year: 1993
Title: Mutant Aspartate Aminotransferase (K258H) without Pyridoxal-5'-Phosphate-Binding Lysine Residue. Structural and Catalytic Properties
Authors: Ziak, M. / Jaeger, J. / Malashkevich, V.N. / Jaussi, R. / Gehring, H. / Jansonius, J.N. / Christen, P.
#2: Journal: Biological Macromolecules and Assemblies / Year: 1987
Title: Structural Basis for Catalysis by Aspartate Aminotransferase
Authors: Jansonius, J.N. / Vincent, M.G.
History
DepositionFeb 28, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 25, 2012Group: Structure summary
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3662
Polymers45,0011
Non-polymers3641
Water5,621312
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7314
Polymers90,0032
Non-polymers7282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7180 Å2
ΔGint-23 kcal/mol
Surface area29820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.100, 91.800, 129.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO A 138 / 2: CIS PROLINE - PRO A 195
3: K258H ACTIVE SITE MUTANT. THE RESIDUE PPD A 411 REPRESENTS THE COVALENT ADDUCT BETWEEN SUBSTRATE L-ASPARTATE AND PYRIDOXAL-5'-PHOSPHATE WITH THE REDUCED ALDIMINE BOND.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE / Aspartate transaminase


Mass: 45001.453 Da / Num. of mol.: 1 / Mutation: K250H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Organ: HEART / Production host: unidentified (others) / References: UniProt: P00508, aspartate transaminase
#2: Chemical ChemComp-PPD / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYLENE)-AMINO]-SUCCINIC ACID / PYRIDOXYL-ASPARTIC ACID-5-MONOPHOSPHATE


Mass: 364.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N2O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsONE MOLECULE OF N-(5'-PHOSPHOPYRIDOXYL)-L-ASPARTATE (PPD) IS BOUND (NON-COVALENTLY) PER SUBUNIT.
Sequence detailsTHE RESIDUES ARE NUMBERED FROM 3 - 410, ACCORDING TO A SEQUENCE ALIGNMENT WITH THE LONGER SEQUENCE ...THE RESIDUES ARE NUMBERED FROM 3 - 410, ACCORDING TO A SEQUENCE ALIGNMENT WITH THE LONGER SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE (SEE U. GRAF-HAUSNER, K.J. WILSON AND P.CHRISTEN (1983), J.BIOL.CHEM. 258, 8813-8826). SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: AATM_CHICK SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE SER 67 PRO A 47 LYS 272 HIS A 258 (MUTATION)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal grow
*PLUS
pH: 7.5 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19-14 %PEG1drop
220 mMsodium phosphate1drop
30.9 M1dropNaCl
420 mMPPxy-Asp1drop
510 mg/mlapoenzyme1drop
618-28 %PEG1reservoir
720 mMsodium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. obs: 18825 / % possible obs: 96.2 % / Num. measured all: 72346 / Rmerge(I) obs: 0.082

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→10 Å / σ(F): 1 /
RfactorNum. reflection
obs0.178 18825
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 24 312 3498
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it5.36
X-RAY DIFFRACTIONp_mcangle_it6.78
X-RAY DIFFRACTIONp_scbond_it8.96
X-RAY DIFFRACTIONp_scangle_it12.48
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.140.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.20.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.73
X-RAY DIFFRACTIONp_staggered_tor20.515
X-RAY DIFFRACTIONp_orthonormal_tor23.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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