Biological Assembly 1  

 3D View: Structure | Electron Density

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: 54.56 kDa 
• Atom Count: 3577 
• Residue Count: 434 
• Unique protein chains: 1

3ASU

Crystal structure of serine dehydrogenase from Escherichia coli

• DOI: 10.2210/pdb3ASU/pdb

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


• Deposited: 2010-12-21 Released: 2011-10-12 
• Deposition Author(s): Yamazawa, R., Nakajima, Y., Yoshimoto, T., Ito, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.230 
• R-Value Work: 0.200 

Literature

Crystal structure of serine dehydrogenase from Escherichia coli: important role of the C-terminal region for closed-complex formation.

Yamazawa, R., Nakajima, Y., Mushiake, K., Yoshimoto, T., Ito, K.

(2011) J Biochem 149: 701-712

• PubMed: 21349860 
• DOI: 10.1093/jb/mvr024
• Primary Citation of Related Structures:  
  3ASU, 3ASV


• PubMed Abstract: 
  

Serine dehydrogenase from Escherichia coli is a homotetrameric enzyme belonging to the short-chain dehydrogenase/reductase (SDR) family. This enzyme catalyses the NADP(+)-dependent oxidation of serine to 2-aminomalonate semialdehyde. The enzyme shows a stereospecificity for β-(3S)-hydroxy acid as a substrate; however, no stereospecificity was observed at the α-carbon. The structures of the ligand-free SerDH and SerDH-NADP(+)-phosphate complex were determined at 1.9 and 2.7 Å resolutions, respectively. The overall structure, including the catalytic tetrad of Asn106, Ser134, Tyr147 and Lys151, shows obvious relationships with other members of the SDR family. The structure of the substrate-binding loop and that of the C-terminal region were disordered in the ligand-free enzyme, whereas these structures were clearly defined in the SerDH-NADP(+) complex as a closed form. Interestingly, the C-terminal region was protruded from the main body and it formed an anti-parallel β-sheet with another C-terminal region on the subunit that is diagonally opposite to that in the tetramer. It is revealed that the C-terminal region possesses the important roles in substrate binding through the stabilization of the substrate-binding loop in the closed form complex. The roles of the C-terminal region along with those of the residues involved in substrate recognition were studied by site-directed mutagenesis.

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Organizational Affiliation: 

Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B	248	Escherichia coli	Mutation(s): 0  Gene Names: EcDH1_2106, YdfG EC: 1.1.1.276

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.230 
• R-Value Work: 0.200 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.79	α = 90
b = 66.79	β = 90
c = 175.9	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-21 
• Released Date: 2011-10-12 
Deposition Author(s): Yamazawa, R., Nakajima, Y., Yoshimoto, T., Ito, K.

Revision History 

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Refinement description