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Basic information

Entry
Database: PDB / ID: 7jsr
TitleCrystal structure of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis
ComponentsNAD-specific glutamate dehydrogenase
KeywordsOXIDOREDUCTASE / large glutamate dehydrogenase / Mycobacterium / metabolism
Function / homology
Function and homology information


glutamate dehydrogenase / glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / L-aspartate:2-oxoglutarate aminotransferase activity
Similarity search - Function
NAD-glutamate dehydrogenase, bacteria / Bacterial NAD-glutamate dehydrogenase, N-terminal / NAD-glutamate dehydrogenase / : / : / : / : / : / : / Bacterial NAD-glutamate dehydrogenase, catalytic domain ...NAD-glutamate dehydrogenase, bacteria / Bacterial NAD-glutamate dehydrogenase, N-terminal / NAD-glutamate dehydrogenase / : / : / : / : / : / : / Bacterial NAD-glutamate dehydrogenase, catalytic domain / Glutamate dehydrogenase, helical motif 1 / Glutamate dehydrogenase, C-terminal / Glutamate dehydrogenase, ACT1 domain / Glutamate dehydrogenase, ACT2 domain / Glutamate dehydrogenase, ACT3 domain / Glutamate dehydrogenase, helical motif 3 / Glutamate dehydrogenase, helical motif 2 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NAD-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.27 Å
AuthorsLazaro, M. / Melero, R. / Huet, C. / Lopez-Alonso, J.P. / Delgado, S. / Dodu, A. / Bruch, E.M. / Abriata, L.A. / Alzari, P.M. / Valle, M. / Lisa, M.N.
Funding support Argentina, 1items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2017-1932 Argentina
CitationJournal: Commun Biol / Year: 2021
Title: 3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme.
Authors: Melisa Lázaro / Roberto Melero / Charlotte Huet / Jorge P López-Alonso / Sandra Delgado / Alexandra Dodu / Eduardo M Bruch / Luciano A Abriata / Pedro M Alzari / Mikel Valle / María-Natalia Lisa /
Abstract: Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180 kDa subunits (L-GDHs) contain long N- ...Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180 kDa subunits (L-GDHs) contain long N- and C-terminal segments flanking the catalytic core. Despite the relevance of L-GDHs in bacterial physiology, the lack of structural data for these enzymes has limited the progress of functional studies. Here we show that the mycobacterial L-GDH (mL-GDH) adopts a quaternary structure that is radically different from that of related low molecular weight enzymes. Intersubunit contacts in mL-GDH involve a C-terminal domain that we propose as a new fold and a flexible N-terminal segment comprising ACT-like and PAS-type domains that could act as metabolic sensors for allosteric regulation. These findings uncover unique aspects of the structure-function relationship in the subfamily of L-GDHs.
History
DepositionAug 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0May 14, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_contact_author / pdbx_modification_feature / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens / struct_ncs_oper / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _entity_src_gen.gene_src_strain / _pdbx_poly_seq_scheme.auth_mon_id ..._entity_src_gen.gene_src_strain / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _struct_ncs_dom.details / _struct_ncs_dom.id / _struct_ncs_dom.pdbx_ens_id / _struct_ncs_ens.id
Description: Model completeness / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-specific glutamate dehydrogenase
B: NAD-specific glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)355,3102
Polymers355,3102
Non-polymers00
Water00
1
A: NAD-specific glutamate dehydrogenase
B: NAD-specific glutamate dehydrogenase

A: NAD-specific glutamate dehydrogenase
B: NAD-specific glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)710,6204
Polymers710,6204
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13210 Å2
ΔGint-21 kcal/mol
Surface area257710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.562, 253.537, 399.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 1 through 13 or resid 30 through 434 or resid 442 through 1588))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11MSEMSESERSERAA1 - 158818 - 1605
d_21MSEMSETYRTYRBB1 - 1318 - 30
d_22ALAALAPROPROBB30 - 43447 - 451
d_23VALVALSERSERBB442 - 1588459 - 1605

NCS oper: (Code: givenMatrix: (-0.321121533216, -0.0647178698174, 0.944824088511), (0.0561720965937, -0.997207413722, -0.0492145261383), (0.945370645022, 0.0372689058739, 0.323860112063)Vector: 97. ...NCS oper: (Code: given
Matrix: (-0.321121533216, -0.0647178698174, 0.944824088511), (0.0561720965937, -0.997207413722, -0.0492145261383), (0.945370645022, 0.0372689058739, 0.323860112063)
Vector: 97.2783214728, 200.919945686, -67.7241352097)

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Components

#1: Protein NAD-specific glutamate dehydrogenase / NAD-GDH / NAD(+)-dependent glutamate dehydrogenase


Mass: 177654.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155, MC2 155 / Gene: gdh, MSMEG_4699, MSMEI_4582 / Production host: Escherichia coli B (bacteria) / References: UniProt: A0R1C2, glutamate dehydrogenase
Has ligand of interestN
Has protein modificationY

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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: 5.44 Å3/Da / Density % sol: 77.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 100 mM sodium cacodylate pH 5.8, 12% v/v glycerol, 1.25 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99187 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 6.27→24.98 Å / Num. obs: 34034 / % possible obs: 98.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 458.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.028 / Rrim(I) all: 0.062 / Net I/σ(I): 10.4
Reflection shellResolution: 6.27→7.01 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1 / Num. unique obs: 9720 / CC1/2: 0.867 / Rpim(I) all: 0.387 / Rrim(I) all: 0.871 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Multiple

Resolution: 6.27→24.98 Å / SU ML: 1.5363 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.2696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2843 1627 5.14 %
Rwork0.2264 30007 -
obs0.2291 31634 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 456.67 Å2
Refinement stepCycle: LAST / Resolution: 6.27→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24096 0 0 0 24096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006524546
X-RAY DIFFRACTIONf_angle_d1.113433366
X-RAY DIFFRACTIONf_chiral_restr0.06013823
X-RAY DIFFRACTIONf_plane_restr0.00694387
X-RAY DIFFRACTIONf_dihedral_angle_d16.67279010
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 6.00273398405 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.27-6.450.47361720.41942393X-RAY DIFFRACTION94.79
6.45-6.660.4631810.4052440X-RAY DIFFRACTION97.54
6.66-6.890.42871910.36222447X-RAY DIFFRACTION98.88
6.89-7.160.3651150.34252509X-RAY DIFFRACTION99.32
7.16-7.480.29841400.29362520X-RAY DIFFRACTION99.11
7.48-7.860.33721360.25722523X-RAY DIFFRACTION98.92
7.86-8.330.3482800.22722549X-RAY DIFFRACTION98.5
8.34-8.950.29211130.20592536X-RAY DIFFRACTION98.92
8.95-9.80.23221140.1932542X-RAY DIFFRACTION99.14
9.8-11.110.20211220.17562526X-RAY DIFFRACTION98.92
11.11-13.610.25391790.19812461X-RAY DIFFRACTION98.43
13.61-24.980.273840.21972561X-RAY DIFFRACTION98.62

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