3JZ4

Crystal structure of E. coli NADP dependent enzyme

• PDB DOI:  https://doi.org/10.2210/pdb3JZ4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-22 Released: 2010-03-16 
• Deposition Author(s): Langendorf, C.G., Key, T.L.G., Fenalti, G., Kan, W.T., Buckle, A.M., Caradoc-Davies, T., Tuck, K.L., Law, R.H.P., Whisstock, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+/enzyme interactions.

Langendorf, C.G., Key, T.L., Fenalti, G., Kan, W.T., Buckle, A.M., Caradoc-Davies, T., Tuck, K.L., Law, R.H., Whisstock, J.C.

(2010) PLoS One 5: e9280-e9280

• PubMed: 20174634 
• DOI: https://doi.org/10.1371/journal.pone.0009280
• Primary Citation of Related Structures:  
  3JZ4


• PubMed Abstract: 
  

In mammals succinic semialdehyde dehydrogenase (SSADH) plays an essential role in the metabolism of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) to succinic acid (SA). Deficiency of SSADH in humans results in elevated levels of GABA and gamma-Hydroxybutyric acid (GHB), which leads to psychomotor retardation, muscular hypotonia, non-progressive ataxia and seizures. In Escherichia coli, two genetically distinct forms of SSADHs had been described that are essential for preventing accumulation of toxic levels of succinic semialdehyde (SSA) in cells.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 209.68 kDa 
• Atom Count: 15,084 
• Modelled Residue Count: 1,924 
• Deposited Residue Count: 1,924 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate-semialdehyde dehydrogenase [NADP+]	A, B, C, D	481	Escherichia coli	Mutation(s): 0  Gene Names: b2661, gabD, JW2636, NA EC: 1.2.1.16 (PDB Primary Data), 1.2.1.79 (UniProt), 1.2.1 (UniProt)
UniProt
Find proteins for P25526 (Escherichia coli (strain K12)) Explore P25526  Go to UniProtKB:  P25526

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], F [auth B], G [auth C], H [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.885	α = 90
b = 151.885	β = 90
c = 165.772	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Langendorf, C.G., Key, T.L.G., Fenalti, G., Kan, W.T., Buckle, A.M., Caradoc-Davies, T., Tuck, K.L., Law, R.H.P., Whisstock, J.C.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance