PDB-8z2b: Crystal structure of apo Aspergillus terreus glutamate dehydrogen...

Basic information

• Entry: Database: PDB / ID: 8z2b
• Title: Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the partially closed conformation (form II)
• Components: Glutamate dehydrogenase
• Keywords: OXIDOREDUCTASE / glutamate dehydrogenase / allostery / cooperativity / Aspergillus / cryo-EM / domain dynamics

Function / homology

Function:

glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / nucleotide binding / cytosol

Domain/homology:

: / Glutamate dehydrogenase / 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

Component:

Glutamate dehydrogenase

• Biological species: Aspergillus terreus (mold)
• Method: X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
• Authors: Godsora, B.K.J. / Bhaumik, P.

Funding support

India, 1items

Organization	Grant number	Country
Science and Engineering Research Board (SERB)	CRG/2021/002404	India

• Citation: Journal: Protein Sci / Year: 2025; Title: Conformational flexibility associated with remote residues regulates the kinetic properties of glutamate dehydrogenase.; Authors: Barsa Kanchan Jyotshna Godsora / Parijat Das / Prasoon Kumar Mishra / Anjali Sairaman / Sandip Kaledhonkar / Narayan S Punekar / Prasenjit Bhaumik / ; Abstract: Glutamate dehydrogenase (GDH) is a pivotal metabolic enzyme in all living organisms, and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric communication during the homotropic effect in GDHs remains poorly understood. In this study, we examined two homologous GDHs, Aspergillus niger GDH (AnGDH) and Aspergillus terreus GDH (AtGDH), with differing substrate utilization kinetics to uncover the factors driving their distinct behavior. We report the crystal structures and first-ever cryo-EM structures of apo- AtGDH and AnGDH that captured arrays of conformational ensembles. A wider mouth opening (~ 21 Å) is observed for the cooperative AnGDH as compared to the non-cooperative AtGDH (~17 Å) in their apo states. A network of interactions related to the substitutions in Domain II influence structural flexibility in these GDHs. Remarkably, we have identified a distant substitution (R246 to S) in Domain II, as a part of this network, which can impact the mouth opening and converts non-cooperative AtGDH into a cooperative enzyme. Our study demonstrates that remote residues can influence structural and kinetic properties in homologous GDHs.

History

Deposition	Apr 12, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 5, 2025	Provider: repository / Type: Initial release

Assembly

Deposited unit

A: Glutamate dehydrogenase

B: Glutamate dehydrogenase

C: Glutamate dehydrogenase

D: Glutamate dehydrogenase

E: Glutamate dehydrogenase

F: Glutamate dehydrogenase

Summary:

• 295 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	295,485	6
Polymers	295,485	6
Non-polymers	0	0
Water	414	23

1

Summary:

• Idetical with deposited unit
• defined by author&software

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	23370 Å2
ΔGint	-14 kcal/mol
Surface area	93100 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	101.690, 101.690, 271.680
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P32

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A
13	7	A
14	7	A
15	8	A
16	8	A
17	9	A
18	9	A
19	10	A
20	10	A
21	11	A
22	11	A
23	12	A
24	12	A
25	13	A
26	13	A
27	14	A
28	14	A
29	15	A
30	15	A

NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TRP / End label comp-ID: TRP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 460 / Label seq-ID: 1 - 460

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6
13	7	7
14	7	7
15	8	8
16	8	8
17	9	9
18	9	9
19	10	10
20	10	10
21	11	11
22	11	11
23	12	12
24	12	12
25	13	13
26	13	13
27	14	14
28	14	14
29	15	15
30	15	15

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

Components

#1: Protein

A B C D E F
Glutamate dehydrogenase

Details:

Mass: 49247.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: gdhA, ATETN484_0007063400 / Production host: Escherichia coli (E. coli) / References: UniProt: T2D1F5

#2: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: N

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.74 ų/Da / Density % sol: 55.19 %
• Crystal grow: Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2, 0.1 M Tris pH 7, and 10% PEG 8000

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
• Detector: Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 17, 2017
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.5418 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.2556
pseudo-merohedral	2	2	K, H, -L	2	0.2478
pseudo-merohedral	3	3	-h,-k,l	3	0.2463
pseudo-merohedral	4	4	-K, -H, -L	4	0.2503

• Reflection: Resolution: 2.85→30 Å / Num. obs: 73339 / % possible obs: 99.9 % / Redundancy: 5.65 % / CC_1/2: 0.98 / Net I/σ(I): 9.3
• Reflection shell: Resolution: 2.85→2.95 Å / Num. unique obs: 7224 / CC_1/2: 0.61

Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XSCALE		data scaling
BALBES		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XVI

5xvi

Resolution: 2.85→29.89 Å / Cor.coef. F_o:F_c: 0.876 / Cor.coef. F_o:F_c free: 0.773 / SU B: 12.687 / SU ML: 0.266 / Cross valid method: FREE R-VALUE / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions

	Rfactor	Num. reflection	% reflection
Rfree	0.2677	3769	5.139 %
Rwork	0.1919	69568	-
all	0.196	-	-
obs	-	69568	99.955 %

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 47.117 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-5.363 Å2	-0 Å2	-0 Å2
2-	-	-5.363 Å2	-0 Å2
3-	-	-	10.725 Å2

Refinement step

Cycle: LAST / Resolution: 2.85→29.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20802	0	0	23	20825

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	21266
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	20082
X-RAY DIFFRACTION	r_angle_refined_deg	1.654	1.803	28788
X-RAY DIFFRACTION	r_angle_other_deg	0.585	1.751	46173
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.835	5	2772
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.258	5	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.858	10	3447
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.418	10	931
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	3126
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	25792
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4980
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	5402
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.215	0.2	21474
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	10818
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	11775
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.219	0.2	634
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.086	0.2	23
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.493	0.2	132
X-RAY DIFFRACTION	r_nbd_other	0.409	0.2	250
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.713	0.2	9
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.247	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	4.032	4.833	11061
X-RAY DIFFRACTION	r_mcbond_other	4.032	4.833	11061
X-RAY DIFFRACTION	r_mcangle_it	6.666	8.678	13824
X-RAY DIFFRACTION	r_mcangle_other	6.666	8.678	13825
X-RAY DIFFRACTION	r_scbond_it	3.145	4.759	10205
X-RAY DIFFRACTION	r_scbond_other	3.145	4.759	10206
X-RAY DIFFRACTION	r_scangle_it	5.396	8.836	14958
X-RAY DIFFRACTION	r_scangle_other	5.396	8.836	14959
X-RAY DIFFRACTION	r_lrange_it	13.355	61.347	91224
X-RAY DIFFRACTION	r_lrange_other	13.354	61.347	91225
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.191	0.05	12809
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.2	0.05	12578
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.212	0.05	12329
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.207	0.05	12336
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.197	0.05	12574
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.198	0.05	12706
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.206	0.05	12497
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.205	0.05	12457
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.199	0.05	12693
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.208	0.05	12483
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.209	0.05	12324
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.2	0.05	12565
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.211	0.05	12231
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.212	0.05	12309
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.207	0.05	12313

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.19123	0.05006
1	2	A	X-RAY DIFFRACTION	Local ncs	0.19123	0.05006
2	3	A	X-RAY DIFFRACTION	Local ncs	0.20044	0.05006
2	4	A	X-RAY DIFFRACTION	Local ncs	0.20044	0.05006
3	5	A	X-RAY DIFFRACTION	Local ncs	0.21208	0.05006
3	6	A	X-RAY DIFFRACTION	Local ncs	0.21208	0.05006
4	7	A	X-RAY DIFFRACTION	Local ncs	0.20696	0.05006
4	8	A	X-RAY DIFFRACTION	Local ncs	0.20696	0.05006
5	9	A	X-RAY DIFFRACTION	Local ncs	0.19681	0.05006
5	10	A	X-RAY DIFFRACTION	Local ncs	0.19681	0.05006
6	11	A	X-RAY DIFFRACTION	Local ncs	0.19762	0.05006
6	12	A	X-RAY DIFFRACTION	Local ncs	0.19762	0.05006
7	13	A	X-RAY DIFFRACTION	Local ncs	0.20614	0.05006
7	14	A	X-RAY DIFFRACTION	Local ncs	0.20614	0.05006
8	15	A	X-RAY DIFFRACTION	Local ncs	0.20515	0.05006
8	16	A	X-RAY DIFFRACTION	Local ncs	0.20515	0.05006
9	17	A	X-RAY DIFFRACTION	Local ncs	0.19867	0.05006
9	18	A	X-RAY DIFFRACTION	Local ncs	0.19867	0.05006
10	19	A	X-RAY DIFFRACTION	Local ncs	0.20827	0.05006
10	20	A	X-RAY DIFFRACTION	Local ncs	0.20827	0.05006
11	21	A	X-RAY DIFFRACTION	Local ncs	0.20937	0.05006
11	22	A	X-RAY DIFFRACTION	Local ncs	0.20937	0.05006
12	23	A	X-RAY DIFFRACTION	Local ncs	0.1998	0.05006
12	24	A	X-RAY DIFFRACTION	Local ncs	0.1998	0.05006
13	25	A	X-RAY DIFFRACTION	Local ncs	0.21079	0.05006
13	26	A	X-RAY DIFFRACTION	Local ncs	0.21079	0.05006
14	27	A	X-RAY DIFFRACTION	Local ncs	0.21245	0.05006
14	28	A	X-RAY DIFFRACTION	Local ncs	0.21245	0.05006
15	29	A	X-RAY DIFFRACTION	Local ncs	0.20681	0.05006
15	30	A	X-RAY DIFFRACTION	Local ncs	0.20681	0.05006

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.85-2.923	0.416	272	0.236	5111	X-RAY DIFFRACTION	99.4458
2.923-3.002	0.335	178	0.211	5109	X-RAY DIFFRACTION	99.9811
3.002-3.089	0.329	266	0.179	4862	X-RAY DIFFRACTION	100
3.089-3.183	0.249	284	0.184	4621	X-RAY DIFFRACTION	100
3.183-3.286	0.269	238	0.164	4576	X-RAY DIFFRACTION	100
3.286-3.4	0.275	260	0.164	4413	X-RAY DIFFRACTION	100
3.4-3.526	0.256	232	0.169	4266	X-RAY DIFFRACTION	100
3.526-3.668	0.253	252	0.161	4074	X-RAY DIFFRACTION	100
3.668-3.828	0.233	178	0.151	3918	X-RAY DIFFRACTION	100
3.828-4.012	0.229	232	0.159	3736	X-RAY DIFFRACTION	100
4.012-4.225	0.226	186	0.161	3622	X-RAY DIFFRACTION	100
4.225-4.476	0.224	156	0.206	3411	X-RAY DIFFRACTION	100
4.476-4.777	0.27	178	0.201	3166	X-RAY DIFFRACTION	100
4.777-5.149	0.248	194	0.193	2973	X-RAY DIFFRACTION	100
5.149-5.623	0.331	154	0.214	2749	X-RAY DIFFRACTION	100
5.623-6.26	0.241	130	0.196	2488	X-RAY DIFFRACTION	100
6.26-7.176	0.34	111	0.214	2220	X-RAY DIFFRACTION	100
7.176-8.664	0.212	122	0.241	1860	X-RAY DIFFRACTION	100
8.664-11.769	0.319	90	0.239	1463	X-RAY DIFFRACTION	99.8714