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- PDB-4k87: Crystal structure of human prolyl-tRNA synthetase (substrate boun... -

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Basic information

Entry
Database: PDB / ID: 4k87
TitleCrystal structure of human prolyl-tRNA synthetase (substrate bound form)
ComponentsProline--tRNA ligase
KeywordsLIGASE / class II tRNA synthetase / Zinc binding / cytosol
Function / homology
Function and homology information


regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation ...regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / GAIT complex / cellular response to type II interferon / RNA stem-loop binding / cellular response to insulin stimulus / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
C-terminal domain of ProRS / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain ...C-terminal domain of ProRS / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Translation Initiation Factor IF3 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / S15/NS1, RNA-binding / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / PROLINE / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsHwang, K.Y. / Son, J.H. / Lee, E.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Conformational changes in human prolyl-tRNA synthetase upon binding of the substrates proline and ATP and the inhibitor halofuginone.
Authors: Son, J. / Lee, E.H. / Park, M. / Kim, J.H. / Kim, J. / Kim, S. / Jeon, Y.H. / Hwang, K.Y.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9964
Polymers60,5481
Non-polymers4483
Water1,15364
1
A: Proline--tRNA ligase
hetero molecules

A: Proline--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,9928
Polymers121,0962
Non-polymers8966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area5980 Å2
ΔGint-17 kcal/mol
Surface area39620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.163, 120.163, 107.098
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Proline--tRNA ligase / Prolyl-tRNA synthetase


Mass: 60548.102 Da / Num. of mol.: 1 / Fragment: UNP residues 1000-1512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS / References: UniProt: P07814, proline-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, 1.0M sodium citrate dibasic trihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2012 / Details: mirrors
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 40003 / Num. obs: 39883 / % possible obs: 99.7 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 52.05 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.3-2.34196.9
2.34-2.38198.5
2.38-2.43198.7
2.43-2.48198.6
2.48-2.53198.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX(Phaser-2.5.1)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K86

4k86


Resolution: 2.301→39.976 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7645 / SU ML: 0.4 / σ(F): 1.39 / Phase error: 30.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 2011 5.04 %
Rwork0.2172 --
obs0.2197 39883 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.76 Å2 / Biso mean: 71.158 Å2 / Biso min: 38.65 Å2
Refinement stepCycle: LAST / Resolution: 2.301→39.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 28 64 4021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114051
X-RAY DIFFRACTIONf_angle_d1.3825486
X-RAY DIFFRACTIONf_dihedral_angle_d15.9831506
X-RAY DIFFRACTIONf_chiral_restr0.247598
X-RAY DIFFRACTIONf_plane_restr0.006699
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3013-2.35880.41611410.3765265599
2.3588-2.42260.37221410.34462656100
2.4226-2.49380.34281430.3222691100
2.4938-2.57430.32061430.30662691100
2.5743-2.66630.35571430.30192688100
2.6663-2.7730.31261420.29012691100
2.773-2.89920.36391410.28542684100
2.8992-3.0520.32361440.27352698100
3.052-3.24320.3231440.25992709100
3.2432-3.49340.30311430.24912700100
3.4934-3.84470.28021460.20322727100
3.8447-4.40050.25361440.17662719100
4.4005-5.54180.19751470.1622758100
5.5418-39.98170.2061490.173280598

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