4ITB

Structure of bacterial enzyme in complex with cofactor and substrate

• PDB DOI:  https://doi.org/10.2210/pdb4ITB/pdb

• Classification: oxidoreductase/substrate
• Organism(s): Synechococcus sp. PCC 7002
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-01-18 Released: 2013-04-24 
• Deposition Author(s): Rhee, S., Park, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.190 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

Structural Basis for a Cofactor-dependent Oxidation Protection and Catalysis of Cyanobacterial Succinic Semialdehyde Dehydrogenase.

Park, J., Rhee, S.

(2013) J Biol Chem 288: 15760-15770

• PubMed: 23589281 
• DOI: https://doi.org/10.1074/jbc.M113.460428
• Primary Citation of Related Structures:  
  4IT9, 4ITA, 4ITB


• PubMed Abstract: 
  

Succinic semialdehyde dehydrogenase (SSADH) from cyanobacterium Synechococcus differs from other SSADHs in the γ-aminobutyrate shunt. Synechococcus SSADH (SySSADH) is a TCA cycle enzyme and completes a 2-oxoglutarate dehydrogenase-deficient cyanobacterial TCA cycle through a detour metabolic pathway. SySSADH produces succinate in an NADP(+)-dependent manner with a single cysteine acting as the catalytic residue in the catalytic loop. Crystal structures of SySSADH were determined in their apo form, as a binary complex with NADP(+) and as a ternary complex with succinic semialdehyde and NADPH, providing details about the catalytic mechanism by revealing a covalent adduct of a cofactor with the catalytic cysteine in the binary complex and a proposed thiohemiacetal intermediate in the ternary complex. Further analyses showed that SySSADH is an oxidation-sensitive enzyme and that the formation of the NADP-cysteine adduct is a kinetically preferred event that protects the catalytic cysteine from H2O2-dependent oxidative stress. These structural and functional features of SySSADH provide a molecular basis for cofactor-dependent oxidation protection in 1-Cys SSADH, which is unique relative to other 2-Cys SSADHs employing a redox-dependent formation of a disulfide bridge.

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Organizational Affiliation: 

Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 101.7 kDa 
• Atom Count: 7,779 
• Modelled Residue Count: 906 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate-semialdehyde dehydrogenase	A, B	456	Synechococcus sp. PCC 7002	Mutation(s): 0  Gene Names: SYNPCC7002_A2771
UniProt
Find proteins for B1XMM6 (Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6)) Explore B1XMM6  Go to UniProtKB:  B1XMM6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], R [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
SSN	D [auth A], S [auth B]	4-oxobutanoic acid C4 H6 O3 UIUJIQZEACWQSV-UHFFFAOYSA-N
EDO	AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.190 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.003	α = 90
b = 115.434	β = 90
c = 180.102	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Rhee, S., Park, J.

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references