8I28 | pdb_00008i28

Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb8I28/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-14 Released: 2023-05-03 
• Deposition Author(s): Jang, J.Y., Chang, J.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.268 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Molecular Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae.

Jang, J., Chang, J.H.

(2023) Int J Mol Sci 24

• PubMed: 36982214 
• DOI: https://doi.org/10.3390/ijms24065139
• Primary Citation Related Structures: 
  8I28


• PubMed Abstract: 
  

  Phosphoserine aminotransferase (PSAT) is a pyridoxal 5'-phosphate-dependent enzyme involved in the second step of the phosphorylated pathway of serine biosynthesis. PSAT catalyzes the transamination of 3-phosphohydroxypyruvate to 3-phosphoserine using L-glutamate as the amino donor. Although structural studies of PSAT have been performed from archaea and humans, no structural information is available from fungi. Therefore, to elucidate the structural features of fungal PSAT, we determined the crystal structure of Saccharomyces cerevisiae PSAT ( Sc PSAT) at a resolution of 2.8 Å. The results demonstrated that the Sc PSAT protein was dimeric in its crystal structure. Moreover, the gate-keeping loop of Sc PSAT exhibited a conformation similar to that of other species. Several distinct structural features in the halide-binding and active sites of Sc PSAT were compared with its homologs. Overall, this study contributes to our current understanding of PSAT by identifying the structural features of fungal PSAT for the first time.

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Organizational Affiliation: 
• Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea.
Department of Biomedical Convergence Science and Technology, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 86.94 kDa 
• Atom Count: 5,253 
• Modeled Residue Count: 670 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine aminotransferase	A, B	395	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SER1, SERC, YOR184W EC: 2.6.1.52
UniProt
Find proteins for P33330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33330  Go to UniProtKB:  P33330

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.268 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.278	α = 90
b = 132.278	β = 90
c = 141.62	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-03 
Deposition Author(s): Jang, J.Y., Chang, J.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection