PDBsum entry 5k8c

Transferase

PDB id: 5k8c

Contents

Protein chain

358 a.a.

Ligands

NAD

PO4 ×2

EDO

Metals

_ZN

_CL ×2

Waters ×439

PDB id:

5k8c

Name:

Transferase

Title:

X-ray structure of kdnb, 3-deoxy-alpha-d-manno-octulosonate 8-oxidase, from shewanella oneidensis

Structure:

3-deoxy-alpha-d-manno-octulosonate 8-oxidase. Chain: a. Engineered: yes

Source:

Shewanella oneidensis (strain mr-1). Organism_taxid: 211586. Strain: mr-1. Gene: kdnb, so_2477. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.85Å R-factor: 0.181 R-free: 0.218

Authors:

H.M.Holden,J.B.Thoden,T.R.Zachman-Brockmeyer

Key ref:

T.R.Zachman-Brockmeyer et al. (2016). Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid. Biochemistry, 55, 4485-4494. PubMed id: 27275764 DOI: 10.1021/acs.biochem.6b00439

Date:

28-May-16 Release date: 15-Jun-16

Protein chain

Q8EEB0  (KDNB_SHEON) -  3-deoxy-alpha-D-manno-octulosonate 8-oxidase from Shewanella oneidensis (strain MR-1)

Seq: 356 a.a.

Struc: 358 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.3.48 - 3-deoxy-alpha-D-manno-octulosonate 8-oxidase.
• Reaction: 3-deoxy-alpha-D-manno-oct-2-ulosonate + O2 = 3,8-dideoxy-8-oxo-alpha-D- manno-octulosonate + H2O2

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

Added reference

DOI no: 10.1021/acs.biochem.6b00439

Biochemistry 55:4485-4494 (2016)

PubMed id: 27275764

Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid.

T.R.Zachman-Brockmeyer, J.B.Thoden, H.M.Holden.

ABSTRACT

8-Amino-3,8-dideoxy-d-manno-octulosonic acid (Kdo8N) is a unique amino sugar that has thus far only been observed on the lipopolysaccharides of marine bacteria belonging to the genus Shewanella. Although its biological function is still unclear, it is thought that the sugar is important for the integrity of the bacterial cell outer membrane. A three-gene cluster required for the biosynthesis of Kdo8N was first identified in Shewanella oneidensis. Here we describe the three-dimensional structures of two of the enzymes required for Kdo8N biosynthesis in S. oneidensis, namely, KdnB and KdnA. The structure of KdnB was solved to 1.85-Å resolution, and its overall three-dimensional architecture places it into the Group III alcohol dehydrogenase superfamily. A previous study suggested that KdnB did not require NAD(P) for activity. Strikingly, although the protein was crystallized in the absence of any cofactors, the electron density map clearly revealed the presence of a tightly bound NAD(H). In addition, a bound metal was observed, which was shown via X-ray fluorescence to be a zinc ion. Unlike other members of the Group III alcohol dehydrogenases, the dinucleotide cofactor in KdnB is tightly bound and cannot be removed without leading to protein precipitation. With respect to KdnA, it is a pyridoxal 5'-phosphate or (PLP)-dependent aminotransferase. For this analysis, the structure of KdnA, trapped in the presence of the external aldimine with PLP and glutamate, was determined to 2.15-Å resolution. The model of KdnA represents the first structure of a sugar aminotransferase that functions on an 8-oxo sugar. Taken together the results reported herein provide new molecular insight into the biosynthesis of Kdo8N.