Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 316.39 kDa 
• Atom Count: 23,954 
• Modelled Residue Count: 2,694 
• Deposited Residue Count: 2,826 
• Unique protein chains: 1

 5GUD

Glutamate dehydrogenase from Corynebacterium glutamicum (alpha-iminoglutarate/NADP+ complex)

• PDB DOI: 10.2210/pdb5GUD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-28 Released: 2017-06-07 
• Deposition Author(s): Tomita, T., Nishiyama, M.
• Funding Organization(s): JSPS

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Crystal structure of the 2-iminoglutarate-bound complex of glutamate dehydrogenase from Corynebacterium glutamicum

Tomita, T., Yin, L., Nakamura, S., Kosono, S., Kuzuyama, T., Nishiyama, M.

(2017) FEBS Lett 591: 1611-1622

• PubMed: 28486765 
• DOI: 10.1002/1873-3468.12667
• Primary Citation of Related Structures:  
  5GUD


• PubMed Abstract: 
  

The NADP ⁺ -dependent glutamate dehydrogenase from Corynebacterium glutamicum (CgGDH) is considered to be one of the key enzymes in the industrial fermentation of glutamate due to its high glutamate-producing activity. We determined the crystal structure of CgGDH complexed with NADP ⁺ and 2-iminoglutarate. Among six subunits of hexameric CgGDH-binding NADP ⁺ , only four subunits bind 2-iminoglutarate in a closed form, while the other two are in an open form. In the closed form, 2-iminoglutarate is bound to the substrate-binding site with the 2-imino group stacked by the nicotinamide ring of the coenzyme, suggesting a prehydride transfer state in a hypothesized reaction scheme with the imino intermediate. We also conducted MD simulations and provide insights into the extreme preference for the glutamate-producing reaction of CgGDH.

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Organizational Affiliation: 

Biotechnology Research Center, The University of Tokyo, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E, F	471	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: APT58_10030
UniProt
Find proteins for A0A0U4QBJ6 (Corynebacterium glutamicum) Explore A0A0U4QBJ6  Go to UniProtKB:  A0A0U4QBJ6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	CA [auth F], H [auth A], M [auth B], P [auth C], T [auth D], X [auth E]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
CIT	W [auth E]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
2IT	BA [auth F], G [auth A], L [auth B], O [auth C]	(2Z)-2-iminopentanedioic acid C5 H7 N O4 UZWLXPOZNAJCJV-UTCJRWHESA-N
K	AA [auth E], DA [auth F], EA [auth F], I [auth A], J [auth A], K [auth A], N [auth B], Q [auth C], R [auth C], S [auth D], U [auth D], V [auth E], Y [auth E], Z [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.226 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.587	α = 90
b = 127.671	β = 106.7
c = 126.627	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Tomita, T., Nishiyama, M.

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Funding Organization	Location	Grant Number
JSPS	Japan	24580137

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references