PDBsum entry 2oge

Transferase

PDB id: 2oge

Contents

Protein chains

368 a.a. *

Ligands

EDO ×21

Metals

_CL ×8

_NA ×2

Waters ×1275

* Residue conservation analysis

PDB id:

2oge

Name:

Transferase

Title:

X-ray structure of s. Venezuelae desv in its internal aldimine form

Structure:

Transaminase. Chain: a, b, c, d. Engineered: yes

Source:

Streptomyces venezuelae. Organism_taxid: 54571. Gene: desv. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.05Å R-factor: 0.162 R-free: 0.234

Authors:

H.M.Holden,E.S.Burgie

Key ref:

E.S.Burgie et al. (2007). Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine. Protein Sci, 16, 887-896. PubMed id: 17456741 DOI: 10.1110/ps.062711007

Date:

05-Jan-07 Release date: 15-May-07

Protein chains

Q9ZGH4  (DESV_STRVZ) -  dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose transaminase from Streptomyces venezuelae

Seq: 379 a.a.

Struc: 368 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.6.1.106 - dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose transaminase.
• Reaction: dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose + 2-oxoglutarate = dTDP-3- dehydro-4,6-dideoxy-alpha-D-glucose + L-glutamate

dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + 2-oxoglutarate = dTDP-3- dehydro-4,6-dideoxy-alpha-D-glucose + L-glutamate

• Cofactor: Pyridoxal 5'-phosphate

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

reference

DOI no: 10.1110/ps.062711007

Protein Sci 16:887-896 (2007)

PubMed id: 17456741

Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine.

E.S.Burgie, J.B.Thoden, H.M.Holden.

ABSTRACT

Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found in certain macrolide antibiotics such as the commonly prescribed erythromycin. Six enzymes are required for its biosynthesis in Streptomyces venezuelae. The focus of this article is DesV, which catalyzes the PLP-dependent replacement of a 3-keto group with an amino functionality in the fifth step of the pathway. For this study the three-dimensional structures of both the internal aldimine and the ketimine intermediate with glutamate were determined to 2.05 A resolution. DesV is a homodimer with each subunit containing 12 alpha-helical regions and 12 beta-strands that together form three layers of sheet. The structure of the internal aldimine demonstrates that the PLP-cofactor is held in place by residues contributed from both subunits (Asp 164 and Gln 167 from Subunit I and Tyr 221 and Asn 235 from Subunit II). When the ketimine intermediate is present in the active site, the loop defined by Gln 225 to Ser 228 from Subunit II closes down upon the active site. The structure of DesV is similar to another sugar-modifying enzyme referred to as PseC. This enzyme is involved in the biosynthesis of pseudaminic acid, which is a sialic acid-like nonulosonate found in the flagellin of Helicobacter pylori. In the case of PseC, however, the amino group is transferred to the C-4 rather than the C-3 position. Details concerning the structural analysis of DesV and a comparison of its molecular architecture to that of PseC are presented.

Selected figure(s)

Figure 3.
Figure 3. The structure of the DesV ketimine intermediate. Electron density corresponding to the ketimine intermediate is presented in

Figure 4.
Figure 4. Superposition of the regions surrounding the internal aldimine versus the ketimine intermediate. The model corresponding

The above figures are reprinted by permission from the Protein Society: Protein Sci (2007, 16, 887-896) copyright 2007.

Figures were selected by an automated process.