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- PDB-3al0: Crystal structure of the glutamine transamidosome from Thermotoga... -

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Basic information

Entry
Database: PDB / ID: 3al0
TitleCrystal structure of the glutamine transamidosome from Thermotoga maritima in the glutamylation state.
Components
  • (Glutamyl-tRNA(Gln) amidotransferase subunit ...) x 2
  • Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
  • tRNAGln
KeywordsLIGASE/RNA / Protein-rna complex / LIGASE-RNA complex
Function / homology
Function and homology information


asparaginyl-tRNA synthase (glutamine-hydrolyzing) activity / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNAGln biosynthesis via transamidation / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / regulation of translational fidelity ...asparaginyl-tRNA synthase (glutamine-hydrolyzing) activity / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNAGln biosynthesis via transamidation / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / regulation of translational fidelity / tRNA binding / translation / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #410 / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E ...Arc Repressor Mutant, subunit A - #410 / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E / GatB/GatE catalytic domain / Glutamyl-tRNA(Gln) amidotransferase subunit B signature. / Asn/Gln amidotransferase / GatB domain / GatB domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 / Glutamate-tRNA synthetase, class I, anticodon-binding domain, subdomain 1 / Arc Repressor Mutant, subunit A - #350 / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Glutamate-tRNA ligase, bacterial/mitochondrial / Glutamyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon binding domain / : / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Amidase / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Helicase, Ruva Protein; domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE / RNA / RNA (> 10) / Glutamyl-tRNA(Gln) amidotransferase subunit C / Glutamyl-tRNA(Gln) amidotransferase subunit A / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Glutamate--tRNA ligase 2
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.368 Å
AuthorsIto, T. / Yokoyama, S.
CitationJournal: Nature / Year: 2010
Title: Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.
Authors: Ito, T. / Yokoyama, S.
History
DepositionJul 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Glutamyl-tRNA(Gln) amidotransferase subunit A
B: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
C: Glutamyl-tRNA(Gln) amidotransferase subunit C,Linker,Glutamate--tRNA ligase 2
E: tRNAGln
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,9196
Polymers201,3784
Non-polymers5412
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19180 Å2
ΔGint-127 kcal/mol
Surface area73660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.954, 125.661, 313.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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Glutamyl-tRNA(Gln) amidotransferase subunit ... , 2 types, 2 molecules AC

#1: Protein Glutamyl-tRNA(Gln) amidotransferase subunit A / Glu-ADT subunit A


Mass: 52594.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: gatA, TM_1272 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q9X0Z9, glutaminyl-tRNA synthase (glutamine-hydrolysing)
#3: Protein Glutamyl-tRNA(Gln) amidotransferase subunit C,Linker,Glutamate--tRNA ligase 2 / Glu-ADT subunit C / Glutamyl-tRNA synthetase 2 / GluRS 2


Mass: 69411.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fused-protein of GatC and GluRS. THE FUSION PROTEIN COMPRISES RESIDUES 2-96 OF GATC, LINKER (GSGSGSGS) AND RESIDUES 1-487 OF GLURS
Source: (gene. exp.) Thermotoga maritima (bacteria), (gene. exp.) synthetic construct (others)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: gatC, TM_0252, gltX2, TM_1875 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q9WY94, UniProt: Q9X2I8, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor, glutamate-tRNA ligase

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Protein / RNA chain , 2 types, 2 molecules BE

#2: Protein Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Asp/Glu-ADT subunit B


Mass: 55514.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: gatB, TM_1273 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q9X100, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#4: RNA chain tRNAGln


Mass: 23858.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 Transcription / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GSU / O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE


Type: L-peptide linking / Mass: 475.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N7O9S

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Details

Sequence detailsTHE CHAIN C IS THE FUSION PROTEIN. IT COMPRISES RESIDUES 2-96 OF GATC, LINKER (GSGSGSGS) AND ...THE CHAIN C IS THE FUSION PROTEIN. IT COMPRISES RESIDUES 2-96 OF GATC, LINKER (GSGSGSGS) AND RESIDUES 1-486 OF GLURS

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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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 2.0M ammonium sulfate, 0.01M magnesium chloride, 0.05M sodium cacodylate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2009 / Details: mirrors
RadiationMonochromator: Rotated-inclined Si(111) double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 40894 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.118 / Net I/σ(I): 15.8
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3028 / Rsym value: 0.396 / % possible all: 70

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.368→48.669 Å / SU ML: 0.4 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 2068 5.07 %random
Rwork0.1952 ---
obs0.1989 40810 92.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.825 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--22.9374 Å20 Å2-0 Å2
2--59.6203 Å2-0 Å2
3----36.6829 Å2
Refinement stepCycle: LAST / Resolution: 3.368→48.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12255 1581 33 0 13869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814303
X-RAY DIFFRACTIONf_angle_d1.31419646
X-RAY DIFFRACTIONf_dihedral_angle_d20.4365674
X-RAY DIFFRACTIONf_chiral_restr0.0972201
X-RAY DIFFRACTIONf_plane_restr0.0072263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.368-3.44640.31171010.23321763X-RAY DIFFRACTION65
3.4464-3.53250.28511160.23852033X-RAY DIFFRACTION74
3.5325-3.6280.34261140.23062250X-RAY DIFFRACTION82
3.628-3.73470.29231350.22792414X-RAY DIFFRACTION88
3.7347-3.85520.3011400.19642483X-RAY DIFFRACTION90
3.8552-3.9930.2521330.1862569X-RAY DIFFRACTION94
3.993-4.15270.23671300.17262715X-RAY DIFFRACTION98
4.1527-4.34160.21751110.15892790X-RAY DIFFRACTION99
4.3416-4.57040.22981380.1492759X-RAY DIFFRACTION100
4.5704-4.85650.2451580.14872783X-RAY DIFFRACTION100
4.8565-5.2310.23091570.16032767X-RAY DIFFRACTION100
5.231-5.75670.27141530.16242781X-RAY DIFFRACTION100
5.7567-6.5880.29191630.17422807X-RAY DIFFRACTION100
6.588-8.29350.23541610.16482851X-RAY DIFFRACTION100
8.2935-48.6740.24551580.18962977X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07810.00460.05190.21610.09670.36680.0085-0.00870.0135-0.046-0.02480.1721-0.33620.04520.00990.86520.1277-0.04140.07480.24320.61050.99140.36-29.7585
22.1382-0.61240.49241.4665-0.07550.0915-0.13380.5605-0.33380.588-0.1695-0.0908-0.07750.0480.20140.1827-0.0323-0.10660.092-0.05840.2253-25.45685.787911.7804
31.55150.15980.63280.08080.16132.1832-0.3905-0.46770.04690.0017-0.42770.0422-0.04710.42520.73730.2203-0.1579-0.04650.48980.23010.5976-31.2492-7.440.181
40.04510.05410.03960.68390.27070.11890.06540.61240.1129-0.0462-0.0478-0.09930.03540.1359-0.03060.9602-0.16230.1791.3126-0.10210.635217.571-21.06115.133
50.977-0.0562-0.93040.3293-0.26980.9461-0.3229-0.57360.18370.16180.3150.10520.28420.6783-0.0617-0.0767-0.2452-0.12150.2864-0.24320.171220.74825.351228.382
60.59270.55060.06581.2351-0.41720.39110.4812-1.10820.2122-0.0083-0.93320.1024-0.02060.35170.49460.4607-0.0574-0.11881.81380.01470.591819.60712.123980.8525
70.5003-0.1660.15230.2998-0.12890.3068-0.0518-0.22120.07930.13880.3087-0.0192-0.0435-0.0529-0.17940.3081-0.1341-0.10680.5557-0.01960.1847-4.94519.007839.2906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or (chain C and resid 3:94) or (chain B and resid 1:300) or (chain B and resid 1001)
2X-RAY DIFFRACTION2chain B and resid 301:417
3X-RAY DIFFRACTION3chain B and resid 418:482
4X-RAY DIFFRACTION4chain C and resid 119:127
5X-RAY DIFFRACTION5(chain C and resid 128:489) or (chain C and resid 1001)
6X-RAY DIFFRACTION6chain C and resid 490:590
7X-RAY DIFFRACTION7chain E

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