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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for P25526 (Escherichia coli (strain K12)) Explore P25526 Go to UniProtKB: P25526
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25526
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations, Refinement description