PDBsum entry 3glc

Lyase

PDB id: 3glc

Contents

Protein chains

(+ 14 more) 276 a.a. *

Ligands

R5P ×20

Waters ×334

* Residue conservation analysis

PDB id:

3glc

Name:

Lyase

Title:

Crystal structure of e. Coli lsrf in complex with ribose-5-phosphate

Structure:

Aldolase lsrf. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t. Fragment: uncharacterized aldolase lsrf. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: b1517, jw1510, lsrf, yneb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.206 R-free: 0.235

Authors:

S.T.Miller,Z.C.Diaz

Key ref:

Z.Diaz et al. (2009). The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF. Plos One, 4, e6820. PubMed id: 19714241

Date:

11-Mar-09 Release date: 08-Sep-09

Protein chains

P76143  (LSRF_ECOLI) -  3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase from Escherichia coli (strain K12)

Seq: 291 a.a.

Struc: 276 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.1.245 - 3-hydroxy-5-phosphooxypentane-2,4-dione thiolase.
• Reaction: dihydroxyacetone phosphate + acetyl-CoA = 3-hydroxy-2,4-dioxopentyl phosphate + CoA

dihydroxyacetone phosphate + acetyl-CoA (Bound ligand (Het Group name = R5P) matches with 71.43% similarity) = 3-hydroxy-2,4-dioxopentyl phosphate + CoA

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

reference

Plos One 4:e6820 (2009)

PubMed id: 19714241

The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.

Z.Diaz, K.B.Xavier, S.T.Miller.

ABSTRACT

Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (alphabeta)(8)-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology with aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase.