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PDBsum entry 1t3d

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1t3d
Jmol
Contents
Protein chains
262 a.a. *
Ligands
CYS ×3
Waters ×416
* Residue conservation analysis
PDB id:
1t3d
Name: Transferase
Title: Crystal structure of serine acetyltransferase from e.Coli at
Structure: Serine acetyltransferase. Chain: a, b, c. Synonym: sat. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: cyse, b3607, c4429, z5034, ecs4485, sf3646, s4122. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.20Å     R-factor:   0.175     R-free:   0.177
Authors: V.E.Pye,A.P.Tingey,R.L.Robson,P.C.E.Moody
Key ref:
V.E.Pye et al. (2004). The structure and mechanism of serine acetyltransferase from Escherichia coli. J Biol Chem, 279, 40729-40736. PubMed id: 15231846 DOI: 10.1074/jbc.M403751200
Date:
26-Apr-04     Release date:   13-Jul-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A9D4  (CYSE_ECOLI) -  Serine acetyltransferase
Seq:
Struc:
273 a.a.
262 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.30  - Serine O-acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
Acetyl-CoA
+
L-serine
Bound ligand (Het Group name = CYS)
matches with 75.00% similarity
= CoA
+ O-acetyl-L-serine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     cellular amino acid biosynthetic process   3 terms 
  Biochemical function     transferase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M403751200 J Biol Chem 279:40729-40736 (2004)
PubMed id: 15231846  
 
 
The structure and mechanism of serine acetyltransferase from Escherichia coli.
V.E.Pye, A.P.Tingey, R.L.Robson, P.C.Moody.
 
  ABSTRACT  
 
Serine acetyltransferase (SAT) catalyzes the first step of cysteine synthesis in microorganisms and higher plants. Here we present the 2.2 A crystal structure of SAT from Escherichia coli, which is a dimer of trimers, in complex with cysteine. The SAT monomer consists of an amino-terminal alpha-helical domain and a carboxyl-terminal left-handed beta-helix. We identify His(158) and Asp(143) as essential residues that form a catalytic triad with the substrate for acetyl transfer. This structure shows the mechanism by which cysteine inhibits SAT activity and thus controls its own synthesis. Cysteine is found to bind at the serine substrate site and not the acetyl-CoA site that had been reported previously. On the basis of the geometry around the cysteine binding site, we are able to suggest a mechanism for the O-acetylation of serine by SAT. We also compare the structure of SAT with other left-handed beta-helical structures.
 
  Selected figure(s)  
 
Figure 3.
FIG. 3. The cysteine binding site and proposed mechanism. a, ball-and-stick representation of the cysteine (pink) binding pocket and key residues (one subunit, orange; adjacent subunit, blue). The main chain is solid-colored, and side chains are transparent; water molecules are represented as cyan spheres, and hydrogen bonds are represented as red dotted lines. b, stereoview of cysteine and water omit map (red) and 2Fo-Fc map of key residues, contoured at 1.2 . c, schematic representation of the proposed mechanism for O-acetylation of serine.
Figure 4.
FIG. 4. Comparison of left-handed -helical structures with SAT. a, serine acetytransferase; b, xenobiotic acetyltransferase (39% identity over 51 aa; Protein Data Bank code 2XAT [PDB] ); c, galactoside O-acetyltransferase (30% identity over 49 aa; Protein Data Bank code 1KRR [PDB] ); d, carbonic anhydrase (34.8% identity over 23 aa; Protein Data Bank code 1QRE [PDB] ); e, tetrahydrodipicilinate N-succinyltransferase (26% identity over 80 aa; Protein Data Bank code 3TDT [PDB] ); f, UDP-N-acetylglucosamine acyltransferase (32.1% identity over 53 aa; Protein Data Bank code 1J2Z [PDB] ). Structures are illustrated as C traces colored from amino terminus (red) to carboxyl terminus (blue).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 40729-40736) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21370978 H.Takahashi, S.Kopriva, M.Giordano, K.Saito, and R.Hell (2011).
Sulfur assimilation in photosynthetic organisms: molecular functions and regulations of transporters and assimilatory enzymes.
  Annu Rev Plant Biol, 62, 157-184.  
21370307 J.F.Trempe, S.Shenker, G.Kozlov, and K.Gehring (2011).
Self-association studies of the bifunctional N-acetylglucosamine-1-phosphate uridyltransferase from Escherichia coli.
  Protein Sci, 20, 745-752.  
20665770 E.J.Rackham, S.Grüschow, A.E.Ragab, S.Dickens, and R.J.Goss (2010).
Pacidamycin biosynthesis: identification and heterologous expression of the first uridyl peptide antibiotic gene cluster.
  Chembiochem, 11, 1700-1709.  
19928859 E.Salsi, A.S.Bayden, F.Spyrakis, A.Amadasi, B.Campanini, S.Bettati, T.Dodatko, P.Cozzini, G.E.Kellogg, P.F.Cook, S.L.Roderick, and A.Mozzarelli (2010).
Design of O-acetylserine sulfhydrylase inhibitors by mimicking nature.
  J Med Chem, 53, 345-356.
PDB codes: 3iqg 3iqh 3iqi
19213732 S.Kumaran, H.Yi, H.B.Krishnan, and J.M.Jez (2009).
Assembly of the cysteine synthase complex and the regulatory role of protein-protein interactions.
  J Biol Chem, 284, 10268-10275.  
18422345 C.M.Bartling, and C.R.Raetz (2008).
Steady-state kinetics and mechanism of LpxD, the N-acyltransferase of lipid A biosynthesis.
  Biochemistry, 47, 5290-5302.  
  19098440 K.C.Kunes, S.C.Clark, D.L.Cox, and R.R.Singh (2008).
Left handed beta helix models for mammalian prion fibrils.
  Prion, 2, 81-90.  
18667421 N.B.Olivier, and B.Imperiali (2008).
Crystal structure and catalytic mechanism of PglD from Campylobacter jejuni.
  J Biol Chem, 283, 27937-27946.
PDB codes: 3bss 3bsw 3bsy
17644602 R.Pinto, J.S.Harrison, T.Hsu, W.R.Jacobs, and T.S.Leyh (2007).
Sulfite reduction in mycobacteria.
  J Bacteriol, 189, 6714-6722.  
17021879 M.Wada, and H.Takagi (2006).
Metabolic pathways and biotechnological production of L-cysteine.
  Appl Microbiol Biotechnol, 73, 48-54.  
16386330 M.Wirtz, and R.Hell (2006).
Functional analysis of the cysteine synthase protein complex from plants: structural, biochemical and regulatory properties.
  J Plant Physiol, 163, 273-286.  
15987896 B.Campanini, F.Speroni, E.Salsi, P.F.Cook, S.L.Roderick, B.Huang, S.Bettati, and A.Mozzarelli (2005).
Interaction of serine acetyltransferase with O-acetylserine sulfhydrylase active site: evidence from fluorescence spectroscopy.
  Protein Sci, 14, 2115-2124.  
15838047 B.Huang, M.W.Vetting, and S.L.Roderick (2005).
The active site of O-acetylserine sulfhydrylase is the anchor point for bienzyme complex formation with serine acetyltransferase.
  J Bacteriol, 187, 3201-3205.
PDB code: 1y7l
16307301 M.Wirtz, and M.Droux (2005).
Synthesis of the sulfur amino acids: cysteine and methionine.
  Photosynth Res, 86, 345-362.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.