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- PDB-2v4i: Structure of a novel N-acyl-enzyme intermediate of an N-terminal ... -

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Basic information

Entry
Database: PDB / ID: 2v4i
TitleStructure of a novel N-acyl-enzyme intermediate of an N-terminal nucleophile (Ntn) hydrolase, OAT2
Components
  • GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
  • GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
KeywordsTRANSFERASE / CYTOPLASM / ACYL ENZYME / NTN HYDROLASE / ACYLTRANSFERASE / ORNITHINE ACETYL TRANSFERASE
Function / homology
Function and homology information


glutamate N-acetyltransferase / glutamate N-acetyltransferase activity / acetyl-CoA:L-glutamate N-acetyltransferase activity / methione N-acyltransferase activity / amino-acid N-acetyltransferase / clavulanic acid biosynthetic process / arginine biosynthetic process / cytoplasm
Similarity search - Function
arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) ...arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) / 4-Layer Sandwich / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate N-acetyltransferase 2 / Arginine biosynthesis bifunctional protein ArgJ 3
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIqbal, A. / Clifton, I.J. / Schofield, C.J.
Citation
Journal: To be Published
Title: Structure of a Novel N-Acyl-Enzyme Intermediate of an N-Terminal Nucleophile (Ntn) Hydrolase, Oat2
Authors: Iqbal, A. / Schofield, C.J. / Clifton, I.J.
#1: Journal: Biochem.J. / Year: 2005
Title: X-Ray Crystal Structure of Ornithine Acetyltransferase from the Clavulanic Acid Biosynthesis Gene Cluster.
Authors: Elkins, J.M. / Kershaw, N.J. / Schofield, C.J.
History
DepositionSep 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
B: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
C: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
D: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
E: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
F: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
G: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
H: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)163,7438
Polymers163,7438
Non-polymers00
Water5,423301
1
A: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
B: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
C: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
D: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)81,8724
Polymers81,8724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-134 kcal/mol
Surface area31310 Å2
MethodPQS
2
E: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
F: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
G: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
H: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)81,8724
Polymers81,8724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-136.1 kcal/mol
Surface area31240 Å2
MethodPQS
Unit cell
Length a, b, c (Å)73.455, 180.163, 60.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 182:383 )
211CHAIN D AND (RESSEQ 182:383 )
311CHAIN F AND (RESSEQ 182:383 )
411CHAIN H AND (RESSEQ 182:383 )
112CHAIN A AND (RESSEQ 8:180 )
212CHAIN C AND (RESSEQ 8:180 )
312CHAIN E AND (RESSEQ 8:180 )
412CHAIN G AND (RESSEQ 8:180 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.994957, 0.097858, -0.022018), (0.098493, -0.994688, 0.029925), (-0.018973, -0.031942, -0.99931)0.27923, -14.2491, -58.7448
2given(0.999994, 0.002881, 0.002065), (0.002884, -0.999995, -0.001312), (0.002061, 0.001318, -0.999997)-36.7103, -4.77987, -58.8733
3given(0.997353, -0.072672, 0.002523), (0.072696, 0.997289, -0.011415), (-0.001686, 0.011568, 0.999932)-36.4612, -13.4586, 0.37556
4given(0.99603, 0.088871, -0.005058), (0.088912, -0.996003, 0.008546), (-0.004278, -0.008962, -0.999951)0.51404, -14.885, -58.1672
5given(0.999968, 0.004027, -0.006899), (0.003982, -0.99997, -0.006611), (-0.006926, 0.006584, -0.999954)-37.0228, -4.97021, -58.6141
6given(0.997039, -0.076901, -0.000166), (0.076901, 0.997033, 0.003419), (-9.7E-5, -0.003421, 0.999994)-36.4117, -13.1599, 0.718

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Components

#1: Protein
GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN / ORNITHINE ACETYL TRANSFERASE / OAT2


Mass: 18089.531 Da / Num. of mol.: 4 / Fragment: RESIDUES 8-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12, PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase
#2: Protein
GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE ACETYL TRANSFERASE / OAT2


Mass: 22846.332 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ACETYLATION OF TERMINAL AMINE OF ALA 181 IN ALL FOUR CHAINS
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12, PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, THR 181 TO ALA ENGINEERED RESIDUE IN CHAIN D, THR 181 TO ALA ...ENGINEERED RESIDUE IN CHAIN B, THR 181 TO ALA ENGINEERED RESIDUE IN CHAIN D, THR 181 TO ALA ENGINEERED RESIDUE IN CHAIN F, THR 181 TO ALA ENGINEERED RESIDUE IN CHAIN H, THR 181 TO ALA
Sequence detailsT181A MUTATION

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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: 2.61 Å3/Da / Density % sol: 52.54 % / Description: NONE
Crystal growpH: 7.5
Details: 1.4 M AMMONIUM SULPHATE, 0.025 M NACL, 0.1M HEPES-NA PH 7.5, 0.1 M NAG, 20 MM CDCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 14, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.471
ReflectionResolution: 2.2→29.7 Å / Num. obs: 79849 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
RIGID-BODYREFINEMENTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VZ6

1vz6


Resolution: 2.2→29.7 Å / σ(F): 1.36 / Phase error: 23.9 / Stereochemistry target values: TWIN_LSQ_F
Details: TWINNING INFORMATION FRACTION 0.471 OPERATOR H,-K,-L
RfactorNum. reflection% reflection
Rfree0.2466 4021 5.04 %
Rwork0.214 --
obs0.2156 79803 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.984 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1--1.5904 Å2-0 Å2-2.2901 Å2
2---15.2885 Å2-0 Å2
3---8.2883 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10852 0 0 301 11153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d011000
X-RAY DIFFRACTIONf_angle_d114976
X-RAY DIFFRACTIONf_dihedral_angle_d14.063836
X-RAY DIFFRACTIONf_chiral_restr0.061808
X-RAY DIFFRACTIONf_plane_restr0.011988
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1490X-RAY DIFFRACTIONPOSITIONAL
12D1490X-RAY DIFFRACTIONPOSITIONAL0.04
13F1490X-RAY DIFFRACTIONPOSITIONAL0.032
14H1490X-RAY DIFFRACTIONPOSITIONAL0.039
21A1215X-RAY DIFFRACTIONPOSITIONAL
22C1215X-RAY DIFFRACTIONPOSITIONAL0.037
23E1215X-RAY DIFFRACTIONPOSITIONAL0.031
24G1215X-RAY DIFFRACTIONPOSITIONAL0.035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23790.32010.27023820X-RAY DIFFRACTION98
2.2379-2.27860.31191840.27973811X-RAY DIFFRACTION98
2.2786-2.32240.31482090.2553783X-RAY DIFFRACTION98
2.3224-2.36980.23582080.24623783X-RAY DIFFRACTION98
2.3698-2.42130.27892020.24333774X-RAY DIFFRACTION98
2.4213-2.47760.26441900.23823776X-RAY DIFFRACTION98
2.4776-2.53950.25191760.23743868X-RAY DIFFRACTION98
2.5395-2.60810.2841890.23623761X-RAY DIFFRACTION98
2.6081-2.68480.30062140.23583788X-RAY DIFFRACTION98
2.6848-2.77140.25211950.22543799X-RAY DIFFRACTION98
2.7714-2.87040.25972080.21243784X-RAY DIFFRACTION98
2.8704-2.98520.22622190.21613762X-RAY DIFFRACTION98
2.9852-3.1210.26691920.21473778X-RAY DIFFRACTION98
3.121-3.28530.24452080.213817X-RAY DIFFRACTION98
3.2853-3.49080.24752020.20523733X-RAY DIFFRACTION98
3.4908-3.75990.23511860.19133807X-RAY DIFFRACTION98
3.7599-4.13740.21361890.18553785X-RAY DIFFRACTION98
4.1374-4.7340.21612330.17343715X-RAY DIFFRACTION98
4.734-5.95640.20151970.19663827X-RAY DIFFRACTION98
5.9564-29.70280.24162020.21433828X-RAY DIFFRACTION98

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