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- PDB-8ar8: Bovine glutamate dehydrogenase in complex with ADP at 2.4 A resolution -

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Basic information

Entry
Database: PDB / ID: 8ar8
TitleBovine glutamate dehydrogenase in complex with ADP at 2.4 A resolution
ComponentsGlutamate dehydrogenase (NAD(P)(+))
KeywordsCYTOSOLIC PROTEIN / Glutamate dehydrogenase / allosteric regulator / ADP
Function / homology
Function and homology information


Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation / positive regulation of insulin secretion / mitochondrial matrix ...Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation / positive regulation of insulin secretion / mitochondrial matrix / nucleotide binding / mitochondrion
Similarity search - Function
NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAleshin, V.A. / Bellinzoni, M.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur Institute France
Citation
Journal: Int J Mol Sci / Year: 2022
Title: Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase.
Authors: Aleshin, V.A. / Bunik, V.I. / Bruch, E.M. / Bellinzoni, M.
#1: Journal: Preprints / Year: 2022
Title: Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase
Authors: Aleshin, V.A. / Bunik, V.I. / Bruch, E.M. / Bellinzoni, M.
History
DepositionAug 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate dehydrogenase (NAD(P)(+))
B: Glutamate dehydrogenase (NAD(P)(+))
C: Glutamate dehydrogenase (NAD(P)(+))
D: Glutamate dehydrogenase (NAD(P)(+))
E: Glutamate dehydrogenase (NAD(P)(+))
F: Glutamate dehydrogenase (NAD(P)(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,85412
Polymers370,2916
Non-polymers2,5636
Water18,3571019
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35120 Å2
ΔGint-144 kcal/mol
Surface area101720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.51, 92.03, 119.57
Angle α, β, γ (deg.)99.35, 106.73, 109.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glutamate dehydrogenase (NAD(P)(+))


Mass: 61715.160 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: A0A140T871, glutamate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20 mM CaCl2, 100 mM Na-acetate buffer (pH 4.6), 30% MPD (2-methyl-2,4-pentanediol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→47.458 Å / Num. obs: 96056 / % possible obs: 89.9 % / Redundancy: 3.4 % / CC1/2: 0.925 / Rpim(I) all: 0.175 / Net I/σ(I): 5
Reflection shellResolution: 2.4→2.484 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4805 / CC1/2: 0.668 / Rpim(I) all: 0.398 / % possible all: 86

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JCZ

3jcz


Resolution: 2.4→47.46 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.88 / Cross valid method: THROUGHOUT / SU R Blow DPI: 2.36 / SU Rfree Blow DPI: 0.302
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 4664 -RANDOM
Rwork0.2037 ---
obs0.2052 96056 76.3 %-
Displacement parametersBiso mean: 41.39 Å2
Baniso -1Baniso -2Baniso -3
1--5.5981 Å21.1333 Å20.2746 Å2
2--6.9256 Å2-6.6996 Å2
3----1.3275 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22937 0 162 1019 24118
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00623592HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7731878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10954SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4034HARMONIC5
X-RAY DIFFRACTIONt_it23592HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3071SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact20393SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion2.76
LS refinement shellResolution: 2.4→2.44 Å
RfactorNum. reflection% reflection
Rfree0.2535 96 -
Rwork0.2459 --
obs0.2463 1922 34.42 %
Refinement TLS params.

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)
12.3072-0.6646-0.33091.02940.12922.93110.03840.15570.27730.1557-0.0040.00050.27730.0005-0.0343-0.118-0.0304-0.0052-0.0439-0.0994-0.0921-21.0622-67.139734.5974
23.321-0.47780.57772.459-0.55052.07810.1512-0.15410.4681-0.15410.2247-0.30150.4681-0.3015-0.3758-0.1522-0.0865-0.09570.0164-0.0590.1079-32.5214-82.81716.1252
30.04550.34010.08771.16881.47738.34330.0842-0.227-0.2246-0.227-0.2578-0.4221-0.2246-0.42210.1737-0.16630.1271-0.05690.2026-0.2142-0.0171-35.6305-52.9553-5.0705
41.8664-1.6782-0.21833.4670.3380.68280.27-0.26340.1637-0.2634-0.21570.15910.16370.1591-0.0543-0.06160.04410.0351-0.005-0.1242-0.1163-14.1885-72.739614.9794
51.03650.20260.32921.1388-0.12641.1694-0.01250.04820.00350.04820.03670.09630.00350.0963-0.0242-0.17110.01340.01320.0775-0.0978-0.10190.9913-38.089519.5774
63.0740.7372-1.09762.0235-0.33512.3366-0.1597-0.36020.1693-0.36020.19540.22930.16930.2293-0.0357-0.1968-0.02030.03230.1932-0.1589-0.17194.6592-44.3884-5.8748
71.41550.14843.20720.52092.13319.95270.04460.11920.54420.1192-0.1021-0.27110.5442-0.27110.0575-0.10840.0109-0.02030.0155-0.1804-0.0296-27.9016-62.3088-6.446
81.90941.2369-0.89112.3614-2.1482.2215-0.0547-0.4237-0.1937-0.42370.0147-0.1634-0.1937-0.16340.04-0.2173-0.0341-0.05550.1737-0.0046-0.1296-10.1612-31.88782.2791
91.45330.63720.21171.49860.40971.26550.02110.0992-0.09160.0992-0.0187-0.1201-0.0916-0.1201-0.0024-0.17280.0480.00290.0649-0.1111-0.1081-36.779-31.74629.2335
102.7658-0.6610.41860.9815-0.04230.98440.0156-0.0932-0.0878-0.0932-0.0282-0.0819-0.0878-0.08190.0126-0.15340.00030.00530.0249-0.1551-0.0551-49.4904-29.06196.0216
110.9790.76391.59963.6494.33676.09430.0579-0.3434-0.1903-0.3434-0.05270.0381-0.19030.0381-0.0052-0.14190.02570.02640.105-0.1191-0.1051-24.3926-50.7162-9.5973
124.1317-0.79150.3663-0.08570.80780.466-0.02260.04230.04580.04230.0058-0.38030.0458-0.38030.0168-0.13430.01570.01220.0178-0.1446-0.0011-46.7405-46.784519.5251
131.5256-0.40470.40050.5888-0.10561.71150.0432-0.1096-0.0522-0.1096-0.03840.0845-0.05220.0845-0.0048-0.1779-0.01090.01490.0751-0.1106-0.09415.2059-28.587141.1551
144.12630.64610.20651.10240.14171.29660.04190.0929-0.16450.09290.02290.1529-0.16450.1529-0.0648-0.19630.00550.02370.0462-0.15820.027818.3744-13.737659.5344
150.4219-0.0791.41810.9341.20963.68070.07010.28020.10890.28020.0665-0.18450.1089-0.1845-0.1365-0.07550.03480.01360.0975-0.1637-0.1175-6.1405-24.225885.037
164.31890.82470.33071.40120.09311.2489-0.1122-0.02920.1039-0.02920.17530.23350.10390.2335-0.063-0.18370.0357-0.00130.1548-0.0772-0.16815.4383-36.009457.247
172.14310.5007-0.22161.53760.98352.27440.06370.09620.25280.0962-0.079-0.05510.2528-0.05510.0153-0.12780.0305-0.01620.005-0.0676-0.1367-10.6111-61.323355.2656
181.6744-0.22710.32972.8429-1.09551.6322-0.05690.0570.27890.057-0.10410.24360.27890.24360.1609-0.09660.08160.0190.0417-0.056-0.05570.5098-63.794780.3267
190.4574-1.1791-1.47032.28763.04829.3818-0.01990.0694-0.26380.06940.2870.6464-0.26380.6464-0.2671-0.14670.0359-0.03030.0727-0.1486-0.05445.2178-28.290582.2406
20-0.5116-0.020.64771.8094-1.02051.06290.03930.15070.02270.15070.053-0.30470.0227-0.3047-0.0923-0.0777-0.00570.07590.1304-0.1052-0.1166-17.4123-55.515374.8418
211.4873-0.02080.37781.61290.36920.9931-0.02310.00120.0370.0012-0.0348-0.1730.037-0.1730.0578-0.18190.02410.01640.0856-0.1392-0.1014-33.0201-29.769153.0769
223.0857-0.8522-0.3572.01940.49222.5826-0.14470.3114-0.02620.31140.0258-0.4617-0.0262-0.46170.1189-0.24240.01340.01510.2265-0.1801-0.1674-36.4843-20.69377.5689
231.27462.26124.55721.2723.72158.68820.01470.3860.47190.386-0.01830.01660.47190.01660.0036-0.0350.0455-0.03120.0778-0.1379-0.121-3.8802-36.218785.5998
241.3215-1.11960.69244.04220.10841.2208-0.0550.267-0.25420.267-0.09730.1643-0.25420.16430.1523-0.23090.0311-0.05920.0496-0.1850.0041-21.2962-14.464364.4
25-5.62861.42944.44092.821-0.01622.8076-0.9637-0.572-0.0326-0.5720.8460.5139-0.03260.51390.1176-0.1790.0762-0.04390.0874-0.21320.2606-12.3233-63.633817.0127
266.3724-12.87262.8946-9.24070.81167.6589-0.4635-0.60470.3925-0.60470.4681-0.7080.3925-0.708-0.0046-0.09950.00590.10190.2915-0.37560.1326-15.8305-33.77869.7298
274.2052-6.07092.2302-4.3383-3.99520.19590.3365-1.4821.9504-1.482-0.19760.21591.95040.2159-0.1389-0.12120.1710.18280.6829-0.0348-0.0307-39.3399-49.731521.4665
283.57493.266-11.93337.17711.8324-1.99180.19992.11970.71162.1197-0.638-0.15130.7116-0.15130.4382-0.15740.02260.05270.4817-0.4480.10668.0314-39.543857.2262
294.5144-4.5122-0.5731-5.32551.4312.63390.07250.4657-1.18890.46570.0733-0.6114-1.1889-0.6114-0.1458-0.35850.0541-0.04180.2954-0.10610.1583-19.1064-49.072668.0469
300.31697.1644-3.31966.7134-1.1507-3.7729-0.22830.3939-0.08760.3939-0.50361.604-0.08761.6040.732-0.24360.12010.10290.3137-0.10670.075-15.5248-19.833159.0046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|64 - A|270 }A64 - 270
2X-RAY DIFFRACTION2{ A|271 - A|451 }A271 - 451
3X-RAY DIFFRACTION3{ A|452 - A|505 }A452 - 505
4X-RAY DIFFRACTION4{ A|506 - A|557 }A506 - 557
5X-RAY DIFFRACTION5{ B|61 - B|270 }B61 - 270
6X-RAY DIFFRACTION6{ B|271 - B|451 }B271 - 451
7X-RAY DIFFRACTION7{ B|452 - B|505 }B452 - 505
8X-RAY DIFFRACTION8{ B|506 - B|557 }B506 - 557
9X-RAY DIFFRACTION9{ C|61 - C|270 }C61 - 270
10X-RAY DIFFRACTION10{ C|271 - C|451 }C271 - 451
11X-RAY DIFFRACTION11{ C|452 - C|505 }C452 - 505
12X-RAY DIFFRACTION12{ C|506 - C|557 }C506 - 557
13X-RAY DIFFRACTION13{ D|66 - D|270 }D66 - 270
14X-RAY DIFFRACTION14{ D|271 - D|451 }D271 - 451
15X-RAY DIFFRACTION15{ D|452 - D|505 }D452 - 505
16X-RAY DIFFRACTION16{ D|506 - D|560 }D506 - 560
17X-RAY DIFFRACTION17{ E|64 - E|270 }E64 - 270
18X-RAY DIFFRACTION18{ E|271 - E|451 }E271 - 451
19X-RAY DIFFRACTION19{ E|452 - E|505 }E452 - 505
20X-RAY DIFFRACTION20{ E|506 - E|556 }E506 - 556
21X-RAY DIFFRACTION21{ F|61 - F|270 }F61 - 270
22X-RAY DIFFRACTION22{ F|271 - F|451 }F271 - 451
23X-RAY DIFFRACTION23{ F|452 - F|505 }F452 - 505
24X-RAY DIFFRACTION24{ F|506 - F|557 }F506 - 557
25X-RAY DIFFRACTION25{ A|601 }A601
26X-RAY DIFFRACTION26{ B|601 }B601
27X-RAY DIFFRACTION27{ C|601 }C601
28X-RAY DIFFRACTION28{ D|601 }D601
29X-RAY DIFFRACTION29{ E|601 }E601
30X-RAY DIFFRACTION30{ F|601 }F601

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