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- PDB-1cla: EVIDENCE FOR TRANSITION-STATE STABILIZATION BY SERINE-148 IN THE ... -

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Basic information

Entry
Database: PDB / ID: 1cla
TitleEVIDENCE FOR TRANSITION-STATE STABILIZATION BY SERINE-148 IN THE CATALYTIC MECHANISM OF CHLORAMPHENICOL ACETYLTRANSFERASE
ComponentsTYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
KeywordsTRANSFERASE (ACYLTRANSFERASE)
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase / chloramphenicol O-acetyltransferase activity / response to antibiotic
Similarity search - Function
Chloramphenicol acetyltransferase, active site / Chloramphenicol acetyltransferase active site. / Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CHLORAMPHENICOL / : / Chloramphenicol acetyltransferase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.34 Å
AuthorsGibbs, M.R. / Leslie, A.G.W.
Citation
Journal: Biochemistry / Year: 1990
Title: Evidence for transition-state stabilization by serine-148 in the catalytic mechanism of chloramphenicol acetyltransferase.
Authors: Lewendon, A. / Murray, I.A. / Shaw, W.V. / Gibbs, M.R. / Leslie, A.G.
#1: Journal: Biochemistry / Year: 1990
Title: Crystal Structure of the Aspartic Acid-199 (Right Arrow) Asparagine Mutant of Chloramphenicol Acetyltransferase to 2.35-Angstroms Resolution: Structural Consequences of Disruption of a Buried Salt Bridge
Authors: Gibbs, M.R. / Moody, P.C.E. / Leslie, A.G.W.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Refined Crystal Structure of Type III Chloramphenicol Acetyltransferase at 1.75 Angstroms Resolution
Authors: Leslie, A.G.W.
#3: Journal: Biochemistry / Year: 1988
Title: Substitutions in the Active Site of Chloramphenicol Acetyltransferase. Role of a Conserved Aspartate
Authors: Lewendon, A. / Murray, I.A. / Kleanthous, C. / Cullis, P.M. / Shaw, W.V.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Structure of Chloramphenicol Acetyltransferase at 1.75-Angstroms Resolution
Authors: Leslie, A.G.W. / Moody, P.C.E. / Shaw, W.V.
#5: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallization of a Type III Chloramphenicol Acetyl Transferase
Authors: Leslie, A.G.W. / Liddell, J.M. / Shaw, W.V.
History
DepositionOct 16, 1989Processing site: BNL
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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 / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET 1 ACTUALLY HAS SEVEN STRANDS. RESIDUES 157 - 162 FORM AN EXTENSION TO THE SIX STRANDED ...SHEET SHEET 1 ACTUALLY HAS SEVEN STRANDS. RESIDUES 157 - 162 FORM AN EXTENSION TO THE SIX STRANDED BETA-SHEET OF AN ADJACENT SHEET WHICH SPANS THE SUBUNIT INTERFACE. N OF ASN 159 IS HYDROGEN BONDED TO O OF SEH 34. THERE IS A WIDE BETA-BULGE INVOLVING RESIDUES LYS 177, TYR 178, AND LEU 187.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4464
Polymers25,0051
Non-polymers4413
Water2,468137
1
A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules

A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules

A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,33912
Polymers75,0163
Non-polymers1,3239
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8950 Å2
ΔGint-80 kcal/mol
Surface area24980 Å2
MethodPISA, PQS
2
A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)152,67924
Polymers150,0336
Non-polymers2,64618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area20300 Å2
ΔGint-223 kcal/mol
Surface area47930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.340, 107.340, 123.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Atom site foot note1: THERE IS A WIDE BETA-BULGE INVOLVING RESIDUES LYS 177, TYR 178, AND LEU 187.
2: RESIDUES 157 - 162 FORM AN EXTENSION TO THE SIX STRANDED BETA-SHEET OF AN ADJACENT SHEET WHICH SPANS THE SUBUNIT INTERFACE.
Components on special symmetry positions
IDModelComponents
11A-222-

CO

21A-223-

CO

31A-310-

HOH

41A-311-

HOH

51A-341-

HOH

61A-365-

HOH

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Components

#1: Protein TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE


Mass: 25005.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P00484, chloramphenicol O-acetyltransferase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-CLM / CHLORAMPHENICOL / Chloramphenicol


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE MUTATED SERINE RESIDUE IS BELIEVED TO PLAY A ROLE IN TRANSITION STATE STABILIZATION (SEE THE ...THE MUTATED SERINE RESIDUE IS BELIEVED TO PLAY A ROLE IN TRANSITION STATE STABILIZATION (SEE THE PAPER CITED ON THE *JRNL* RECORDS ABOVE). THE SER 148 TO ALA MUTANT SHOWS A SIGNIFICANT LOSS IN ACTIVITY (K=CAT= REDUCED 53-FOLD) BUT IS ESSENTIALLY ISOSTRUCTURAL WITH THE WILD-TYPE ENZYME.
Sequence detailsTHE NUMBERING SCHEME ADOPTED IS BASED ON THE ALIGNMENT OF A NUMBER OF CAT SEQUENCES. FOR THE TYPE ...THE NUMBERING SCHEME ADOPTED IS BASED ON THE ALIGNMENT OF A NUMBER OF CAT SEQUENCES. FOR THE TYPE III ENZYME WHOSE COORDINATES ARE PRESENTED IN THIS ENTRY, MET 6 IS THE N-TERMINAL RESIDUE AND THERE IS NO RESIDUE NUMBER 79.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.3 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1buttom
210 mMMES1buttom
34 %MPD1reservoir
410 mMMES1reservoir
51 mMchloramphenicol1reservoir
60.5 mMhexa amminecobalt chloride1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.34 Å / Rmerge(I) obs: 0.033

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.172 / Highest resolution: 2.34 Å
Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING THE REFINED 1.75 ANGSTROMS RESOLUTION STRUCTURE OF THE WILD TYPE ENZYME AS A MODEL.
Refinement stepCycle: LAST / Highest resolution: 2.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 22 137 1863
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
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_restr00.02
X-RAY DIFFRACTIONp_chiral_restr0.10.15
X-RAY DIFFRACTIONp_singtor_nbd0.10.2
X-RAY DIFFRACTIONp_multtor_nbd0.20.2
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
Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d0.043
X-RAY DIFFRACTIONp_planar_d0.056
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.17

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