PDBsum entry 1s3h

Transferase

PDB id: 1s3h

Contents

Protein chain

472 a.a. *

Metals

_CO

Waters ×1

* Residue conservation analysis

PDB id:

1s3h

Name:

Transferase

Title:

Propionibacterium shermanii transcarboxylase 5s subunit a59t

Structure:

Transcarboxylase 5s subunit. Chain: a. Engineered: yes. Mutation: yes

Source:

Propionibacterium freudenreichii subsp. Shermanii. Organism_taxid: 1752. Strain: subsp. Shermanii. Gene: 5s. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.205 R-free: 0.250

Authors:

P.R.Hall,R.Zheng,L.Antony,M.Pusztai-Carey,P.R.Carey,V.C.Yee

Key ref:

P.R.Hall et al. (2004). Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit. EMBO J, 23, 3621-3631. PubMed id: 15329673 DOI: 10.1038/sj.emboj.7600373

Date:

13-Jan-04 Release date: 07-Sep-04

Protein chain

Q70AC7  (5S_PROFR) -  Methylmalonyl-CoA carboxyltransferase 5S subunit from Propionibacterium freudenreichii subsp. shermanii

Seq: 505 a.a.

Struc: 472 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.3.1 - methylmalonyl-CoA carboxytransferase.
• Reaction: (S)-methylmalonyl-CoA + pyruvate = propanoyl-CoA + oxaloacetate
• Cofactor: Biotin; Cobalt cation; Zn(2+)

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

reference

DOI no: 10.1038/sj.emboj.7600373

EMBO J 23:3621-3631 (2004)

PubMed id: 15329673

Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit.

P.R.Hall, R.Zheng, L.Antony, M.Pusztai-Carey, P.R.Carey, V.C.Yee.

ABSTRACT

Transcarboxylase is a 1.2 million Dalton (Da) multienzyme complex from Propionibacterium shermanii that couples two carboxylation reactions, transferring CO(2)(-) from methylmalonyl-CoA to pyruvate to yield propionyl-CoA and oxaloacetate. Crystal structures of the 5S metalloenzyme subunit, which catalyzes the second carboxylation reaction, have been solved in free form and bound to its substrate pyruvate, product oxaloacetate, or inhibitor 2-ketobutyrate. The structure reveals a dimer of beta(8)alpha(8) barrels with an active site cobalt ion coordinated by a carbamylated lysine, except in the oxaloacetate complex in which the product's carboxylate group serves as a ligand instead. 5S and human pyruvate carboxylase (PC), an enzyme crucial to gluconeogenesis, catalyze similar reactions. A 5S-based homology model of the PC carboxyltransferase domain indicates a conserved mechanism and explains the molecular basis of mutations in lactic acidemia. PC disease mutations reproduced in 5S result in a similar decrease in carboxyltransferase activity and crystal structures with altered active sites.

Selected figure(s)

Figure 5.
Figure 5 Active sites of 5S complexes. The free 5S active site is shown with its Lys[C]184 (ball-and-stick with gray carbon atoms and bonds), cobalt ion (pink sphere), water ligands (red spheres), and side chains of residues which interact with either the cobalt ion or bound ligand. Superimposed are oxaloacetate (yellow), pyruvate (pale pink), and 2-ketobutyrate (cyan) ligands from their respective complexes.

Figure 6.
Figure 6 Active sites of 5S mutants. (A) Composite 5S active site showing the 5S-A59T crystal structure. The Thr59 side chain (orange and red ball-and-stick) interacts with Gln26, which in the complex structures forms hydrogen bonds with the bound ligands. For reference, oxaloacetate (yellow, as bound in 5S-oxal) and residues with which it interacts (Arg22 and Gln26), Met186 (gray, conformation in free 5S; pale pink, conformation in 5S-oxal), cobalt ion (pink sphere), and carbamylated Lys[C]184 are also shown. The orientation of this figure is related to that of Figure 5 by 90° rotation about the vertical axis combined with 90° rotation about the horizontal axis. (B) Composite 5S active site showing the 5S-M186I crystal structure. The I186 side chain (cyan ball-and-stick structure) would be expected to make close contacts with substrate or product; oxaloacetate (yellow, as bound in 5S-oxal) and Ala59 are shown for reference.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 3621-3631) copyright 2004.

Figures were selected by an automated process.