PDBsum entry 3a2b

Transferase

PDB id: 3a2b

Contents

Protein chain

392 a.a. *

Ligands

SER-PLP

Waters ×285

* Residue conservation analysis

PDB id:

3a2b

Name:

Transferase

Title:

Crystal structure of serine palmitoyltransferase from sphingobacterium multivorum with substrate l-serine

Structure:

Serine palmitoyltransferase. Chain: a. Engineered: yes

Source:

Sphingobacterium multivorum. Organism_taxid: 28454. Strain: gtc97. Gene: spt. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.211 R-free: 0.270

Authors:

A.Okamoto,J.Hoseki

Key ref:

H.Ikushiro et al. (2009). Structural insights into the enzymatic mechanism of serine palmitoyltransferase from Sphingobacterium multivorum. J Biochem (tokyo), 146, 549-562. PubMed id: 19564159

Date:

09-May-09 Release date: 14-Jul-09

Protein chain

A7BFV6  (SPT_SPHMU) -  Serine palmitoyltransferase from Sphingobacterium multivorum

Seq: 399 a.a.

Struc: 392 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.3.1.- - ?????
• Enzyme class 2: E.C.2.3.1.47 - 8-amino-7-oxononanoate synthase.
• Reaction: 6-carboxyhexanoyl-[ACP] + L-alanine + H⁺ = (8S)-8-amino-7-oxononanoate + holo-[ACP] + CO2

6-carboxyhexanoyl-[ACP] + L-alanine + H(+) (Bound ligand (Het Group name = SER) matches with 85.71% similarity) = (8S)-8-amino-7-oxononanoate + holo-[ACP] + CO2

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

• Enzyme class 3: E.C.2.3.1.50 - serine C-palmitoyltransferase.
• Reaction: L-serine + hexadecanoyl-CoA + H⁺ = 3-oxosphinganine + CO2 + CoA

L-serine + hexadecanoyl-CoA + H(+) (Bound ligand (Het Group name = SER) corresponds exactly) = 3-oxosphinganine + CO2 + CoA

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

J Biochem (tokyo) 146:549-562 (2009)

PubMed id: 19564159

Structural insights into the enzymatic mechanism of serine palmitoyltransferase from Sphingobacterium multivorum.

H.Ikushiro, M.M.Islam, A.Okamoto, J.Hoseki, T.Murakawa, S.Fujii, I.Miyahara, H.Hayashi.

ABSTRACT

Serine palmitoyltransferase (SPT) is a key enzyme of sphingolipid biosynthesis and catalyses the pyridoxal 5'-phosphate (PLP)-dependent decarboxylative condensation reaction of l-serine with palmitoyl-CoA to generate 3-ketodihydrosphingosine. The crystal structure of SPT from Sphingobacterium multivorum GTC97 complexed with l-serine was determined at 2.3 A resolution. The electron density map showed the Schiff base formation between l-serine and PLP in the crystal. Because of the hydrogen bond formation with His138, the orientation of the Calpha-H bond of the PLP-l-serine aldimine was not perpendicular to the PLP-Schiff base plane. This conformation is unfavourable for the alpha-proton abstraction by Lys244 and the reaction is expected to stop at the PLP-l-serine aldimine. Structural modelling of the following intermediates indicated that His138 changes its hydrogen bond partner from the carboxyl group of l-serine to the carbonyl group of palmitoyl-CoA upon the binding of palmitoyl-CoA, making the l-serine Calpha-H bond perpendicular to the PLP-Schiff base plane. These crystal and model structures well explained the observations on bacterial SPTs that the alpha-deprotonation of l-serine occurs only in the presence of palmitoyl-CoA. This study provides the structural evidence that directly supports our proposed mechanism of the substrate synergism in the SPT reaction.