5YW0

Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with succinate and Fe(III)

Summary for 5YW0

• Entry DOI: 10.2210/pdb5yw0/pdb
• Related: 5Y9Y 5YVZ
• Descriptor: Uncharacterized protein KdoO, TETRAETHYLENE GLYCOL, FE (III) ION, ... (7 entities in total)
• Functional Keywords: fe(ii)/o2/alphaketoglutarate dependent dioxygenase, kdo2-lipid a dioxygenase, deoxysugar dioxygenase, lps biosynthesis, biosynthetic protein
• Biological source: Methylacidiphilum infernorum (isolate V4)
• Total number of polymer chains: 1
• Total formula weight: 37712.65

Authors

Chung, H.S.,Pemble, C.W.,Joo, S.H.,Raetz, C.R. (deposition date: 2017-11-28, release date: 2018-09-05, Last modification date: 2024-03-27)

Primary citation

Joo, S.H.,Pemble, C.W.,Yang, E.G.,Raetz, C.R.H.,Chung, H.S.
Biochemical and Structural Insights into an Fe(II)/ alpha-Ketoglutarate/O2-Dependent Dioxygenase, Kdo 3-Hydroxylase (KdoO).
J. Mol. Biol., 430:4036-4048, 2018

PubMed Abstract: During lipopolysaccharide biosynthesis in several pathogens, including Burkholderia and Yersinia, 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) 3-hydroxylase, otherwise referred to as KdoO, converts Kdo to d-glycero-d-talo-oct-2-ulosonic acid (Ko) in an Fe(II)/α-ketoglutarate (α-KG)/O-dependent manner. This conversion renders the bacterial outer membrane more stable and resistant to stresses such as an acidic environment. KdoO is a membrane-associated, deoxy-sugar hydroxylase that does not show significant sequence identity with any known enzymes, and its structural information has not been previously reported. Here, we report the biochemical and structural characterization of KdoO, Minf_1012 (Kdo), from Methylacidiphilum infernorum V4. The de novo structure of Kdo apoprotein indicates that KdoO consists of 13 α helices and 11 β strands, and has the jelly roll fold containing a metal binding motif, HXDXH. Structures of Kdo bound to Co(II), Kdo bound to α-KG and Fe(III), and Kdo bound to succinate and Fe(III), in addition to mutagenesis analysis, indicate that His146, His260, and Asp148 play critical roles in Fe(II) binding, while Arg127, Arg162, Arg174, and Trp176 stabilize α-KG. It was also observed that His225 is adjacent to the active site and plays an important role in the catalysis of KdoO without affecting substrate binding, possibly being involved in oxygen activation. The crystal structure of KdoO is the first completed structure of a deoxy-sugar hydroxylase, and the data presented here have provided mechanistic insights into deoxy-sugar hydroxylase, KdoO, and lipopolysaccharide biosynthesis.

PubMed: 30092253
DOI: 10.1016/j.jmb.2018.07.029

Experimental method

X-RAY DIFFRACTION (1.49 Å)