PDBsum entry 3mpb

Isomerase

PDB id

3mpb

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Contents

			Protein chains

					226 a.a. *

			Ligands

					ACT ×2


					FRU ×2


					GOL

			Metals

					_MN ×2

			Waters ×281

* Residue conservation analysis

PDB id:

3mpb

Links

Name:

Isomerase

Title:

Z5688 from e. Coli o157:h7 bound to fructose

Structure:

Sugar isomerase. Chain: a, b. Synonym: uncharacterized protein ecs5070. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83334. Strain: o157:h7 edl933. Gene: ecs5070, z5688. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.91Å

R-factor:

0.191

R-free:

0.233

Authors:

L.M.Van Staalduinen,Z.Jia,Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)

Key ref:

L.M.van Staalduinen et al. (2010). Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157:H7. J Mol Biol, 401, 866-881. PubMed id: 20615418

Date:

26-Apr-10

Release date:

21-Jul-10

PROCHECK

	Headers

	References

Protein chains

Q8X5Q7 (Q8X5Q7_ECO57) - D-lyxose ketol-isomerase from Escherichia coli O157:H7

Seq: Struc:					227 a.a. 226 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.5.3.1.15 - D-lyxose ketol-isomerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

D-lyxose = D-xylulose

D-lyxose
Bound ligand (Het Group name = FRU)
matches with 83.33% similarity

D-xylulose

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

Added reference

	J Mol Biol 401:866-881 (2010)
PubMed id: 20615418

Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157:H7.
L.M.van Staalduinen, C.S.Park, S.J.Yeom, M.A.Adams-Cioaba, D.K.Oh, Z.Jia.

ABSTRACT

Prokaryotes can use a variety of sugars as carbon sources in order to provide a selective survival advantage. The gene z5688 found in the pathogenic E. coli O157:H7 encodes a 'hypothetical' protein of unknown function. Sequence analysis identified the gene product as a putative member of the cupin superfamily of proteins, but no other functional information was known. We have determined the crystal structure of the Z5688 protein at 1.6 A resolution and identified the protein as a novel E. coli sugar isomerase (EcSI) through overall fold analysis and secondary structure matching. Extensive substrate screening revealed that EcSI is capable of acting on d-lyxose and d-mannose. The complex structure of EcSI with fructose allowed the identification of key active site residues, and mutagenesis confirmed their importance. The structure of EcSI also suggested a novel mechanism for substrate binding and product release in a cupin sugar isomerase. Supplementation of a non-pathogenic E. coli strain with EcSI enabled cell growth on the rare pentose d-lyxose.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21520290

J.Marles-Wright, and R.J.Lewis (2011).
The structure of a D-lyxose isomerase from the σ(B) regulon of Bacillus subtilis.

Proteins, 79, 2015-2019.

PDB code:

2y0o

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 code is shown on the right.