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- PDB-2pid: Crystal structure of human mitochondrial tyrosyl-tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 2pid
TitleCrystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN-SUBSTRATE COMPLEX / ATP-binding / Mitochondrion / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


mitochondrial tyrosyl-tRNA aminoacylation / L-tyrosine binding / Mitochondrial tRNA aminoacylation / tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / tRNA binding / nuclear body / mitochondrial matrix / translation ...mitochondrial tyrosyl-tRNA aminoacylation / L-tyrosine binding / Mitochondrial tRNA aminoacylation / tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / tRNA binding / nuclear body / mitochondrial matrix / translation / protein homodimerization activity / mitochondrion / RNA binding / ATP binding / cytosol
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / RNA-binding S4 domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / Tyrosine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBonnefond, L. / Frugier, M. / Touze, E. / Lorber, B. / Florentz, C. / Giege, R. / Sauter, C. / Rudinger-Thirion, J.
Citation
Journal: Structure / Year: 2007
Title: Crystal Structure of Human Mitochondrial Tyrosyl-tRNA Synthetase Reveals Common and Idiosyncratic Features.
Authors: Bonnefond, L. / Frugier, M. / Touze, E. / Lorber, B. / Florentz, C. / Giege, R. / Sauter, C. / Rudinger-Thirion, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Tyrosyl-tRNA synthetase: the first crystallization of a human mitochondrial aminoacyl-tRNA synthetase
Authors: Bonnefond, L. / Frugier, M. / Touze, E. / Lorber, B. / Florentz, C. / Giege, R. / Rudinger-Thirion, J. / Sauter, C.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase
B: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9444
Polymers79,9252
Non-polymers1,0192
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-21 kcal/mol
Surface area27180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.000, 62.400, 194.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosyl-tRNA synthetase / Tyrosine-tRNA ligase / TyrRS


Mass: 39962.371 Da / Num. of mol.: 2 / Fragment: Residues 28-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YARS2 / Plasmid: pQE70-mt-TyrRS-[Delta]S4 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9Y2Z4, tyrosine-tRNA ligase
#2: Chemical ChemComp-YSA / 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / TYROSYLADENYLATE


Mass: 509.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O8S / Details: 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 3 mg/ml protein, 30% (m/v) PEG 4000, 200 mM Ammonium acetate, 100 mM sodium acetate pH 4.6, 100 mM Tris-HCl pH 7.5, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97565
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 34168 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 19.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 8.2 / Rsym value: 0.427 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VBM

1vbm


Resolution: 2.2→19.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2251160.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1700 5 %RANDOM
Rwork0.193 ---
obs0.193 34156 99.6 %-
all-34156 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.68 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.6 Å20 Å20 Å2
2--3.12 Å20 Å2
3----10.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 70 90 5262
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.832
X-RAY DIFFRACTIONc_mcangle_it3.842.5
X-RAY DIFFRACTIONc_scbond_it4.22.5
X-RAY DIFFRACTIONc_scangle_it5.83
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.309 171 5.2 %
Rwork0.228 3132 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3YSA.PARAMYSA.TOP

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