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- PDB-1aaw: THE STRUCTURAL BASIS FOR THE ALTERED SUBSTRATE SPECIFICITY OF THE... -

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Basic information

Entry
Database: PDB / ID: 1aaw
TitleTHE STRUCTURAL BASIS FOR THE ALTERED SUBSTRATE SPECIFICITY OF THE R292D ACTIVE SITE MUTANT OF ASPARTATE AMINOTRANSFERASE FROM E. COLI
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE
Function / homology
Function and homology information


L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytoplasm / 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
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsAlmo, S.C. / Smith, D.L. / Danishefsky, A.T. / Ringe, D.
Citation
Journal: Protein Eng. / Year: 1994
Title: The structural basis for the altered substrate specificity of the R292D active site mutant of aspartate aminotransferase from E. coli.
Authors: Almo, S.C. / Smith, D.L. / Danishefsky, A.T. / Ringe, D.
#1: Journal: Biochemistry / Year: 1991
Title: Activity and Structure of the Active Site Mutants R386Y and R386F of Escherichia Coli Aspartate Aminotransferase
Authors: Danishefsky, A.T. / Onnufer, J.J. / Petsko, G.A. / Ringe, D.
#2: Journal: Biochemistry / Year: 1989
Title: 2.8 Angstroms Resolution Crystal Structure of an Active Site Mutant of Aspartate Aminotransferase from Escherichia Coli
Authors: Smith, D.L. / Almo, S.C. / Toney, M.D. / Ringe, D.
History
DepositionJul 13, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8662
Polymers43,6191
Non-polymers2471
Water543
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7334
Polymers87,2382
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7430 Å2
ΔGint-24 kcal/mol
Surface area30530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)156.800, 86.900, 80.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: ALA 20 - PRO 21 OMEGA ANGLE = 258.164 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO 140 / 3: CIS PROLINE - PRO 196
4: ASP 200 - PRO 201 OMEGA ANGLE = 115.757 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: RESIDUE PLP 409 IS BOUND TO LYS 258 FORMING A PROTONATED SCHIFF BASE LINKAGE BETWEEN NZ LYS 258 AND C4A PLP 409.
DetailsTHE MOLECULE IS A DIMER. TO GENERATE THE OTHER CHAIN ONE MUST APPLY THE CRYSTALLOGRAPHIC SYMMETRY OPERATION (X, 86.9-Y, 80.0-Z) TO THE COORDINATES IN THIS ENTRY.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 43619.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion / Details: referred to J.Mol.Biol. 191.301-302 1986
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
20.025 Msodium phosphate1drop
30.02 mMPLP1drop
450 %satammonium sulfate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 15069 / % possible obs: 72 %

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.208 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 15 3 3087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d6
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 5 Å / Num. reflection obs: 15069 / σ(I): 2 / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg46
X-RAY DIFFRACTIONp_planar_d0.070.104

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