PDBsum entry 3dr4

Transferase

PDB id: 3dr4

Contents

Protein chains

364 a.a. *

Ligands

G4M ×4

EDO ×2

Waters ×1259

* Residue conservation analysis

PDB id:

3dr4

Name:

Transferase

Title:

Gdp-perosamine synthase k186a mutant from caulobacter crescentus with bound sugar ligand

Structure:

Putative perosamine synthetase. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Caulobacter crescentus. Organism_taxid: 155892. Strain: cb15. Gene: per. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å R-factor: 0.166 R-free: 0.238

Authors:

H.M.Holden,P.D.Cook,A.E.Carney

Key ref:

P.D.Cook et al. (2008). Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase. Biochemistry, 47, 10685-10693. PubMed id: 18795799

Date:

10-Jul-08 Release date: 14-Oct-08

Protein chains

Q9A9H3  (GDPPS_CAUVC) -  GDP-perosamine synthase from Caulobacter vibrioides (strain ATCC 19089 / CB15)

Seq: 371 a.a.

Struc: 364 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.6.1.102 - GDP-perosamine synthase.
• Reaction: GDP-alpha-D-perosamine + 2-oxoglutarate = GDP-4-dehydro-alpha-D-rhamnose + L-glutamate

GDP-alpha-D-perosamine (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + 2-oxoglutarate = GDP-4-dehydro-alpha-D-rhamnose + L-glutamate

• Cofactor: Pyridoxal 5'-phosphate

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

reference

Biochemistry 47:10685-10693 (2008)

PubMed id: 18795799

Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase.

P.D.Cook, A.E.Carney, H.M.Holden.

ABSTRACT

Perosamine (4-amino-4,6-dideoxy- d-mannose), or its N-acetylated form, is one of several dideoxy sugars found in the O-antigens of such infamous Gram-negative bacteria as Vibrio cholerae O1 and Escherichia coli O157:H7. It is added to the bacterial O-antigen via a nucleotide-linked version, namely GDP-perosamine. Three enzymes are required for the biosynthesis of GDP-perosamine starting from mannose 1-phosphate. The focus of this investigation is GDP-perosamine synthase from Caulobacter crescentus, which catalyzes the final step in GDP-perosamine synthesis, the conversion of GDP-4-keto-6-deoxymannose to GDP-perosamine. The enzyme is PLP-dependent and belongs to the aspartate aminotransferase superfamily. It contains the typically conserved active site lysine residue, which forms a Schiff base with the PLP cofactor. Two crystal structures were determined for this investigation: a site-directed mutant protein (K186A) complexed with GDP-perosamine and the wild-type enzyme complexed with an unnatural ligand, GDP-3-deoxyperosamine. These structures, determined to 1.6 and 1.7 A resolution, respectively, revealed the manner in which products, and presumably substrates, are accommodated within the active site pocket of GDP-perosamine synthase. Additional kinetic analyses using both the natural and unnatural substrates revealed that the K m for the unnatural substrate was unperturbed relative to that of the natural substrate, but the k cat was lowered by a factor of approximately 200. Taken together, these studies shed light on why GDP-perosamine synthase functions as an aminotransferase whereas another very similar PLP-dependent enzyme, GDP-4-keto-6-deoxy- d-mannose 3-dehydratase or ColD, catalyzes a dehydration reaction using the same substrate.