5GUD

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


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 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

    Biotechnology Research Center, The University of Tokyo, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate dehydrogenase
A, B, C, D, E, F
A, B, C, D, E, F
471Corynebacterium glutamicumMutation(s): 0 
Gene Names: APT58_10030
UniProt
Find proteins for A0A0U4QBJ6 (Corynebacterium glutamicum)
Explore A0A0U4QBJ6 
Go to UniProtKB:  A0A0U4QBJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U4QBJ6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
CA [auth F],
H [auth A],
M [auth B],
P [auth C],
T [auth D],
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
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
W [auth E]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
2IT
Query on 2IT

Download Ideal Coordinates CCD File 
BA [auth F],
G [auth A],
L [auth B],
O [auth C]
(2Z)-2-iminopentanedioic acid
C5 H7 N O4
UZWLXPOZNAJCJV-UTCJRWHESA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth E],
DA [auth F],
EA [auth F],
I [auth A],
J [auth A],
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
 Ligand Interaction
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 = 92.587α = 90
b = 127.671β = 106.7
c = 126.627γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan24580137

Revision History  (Full details and data files)

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