PDBsum entry 2iu8

Transferase

PDB id: 2iu8

Contents

Protein chains

346 a.a. *

Ligands

SO4 ×6

PLM ×3

EDO

BME

UD1

Waters ×495

* Residue conservation analysis

PDB id:

2iu8

Name:

Transferase

Title:

Chlamydia trachomatis lpxd with 25mm udpglcnac (complex i)

Structure:

Udp-3-o-[3-hydroxymyristoyl] glucosamine n-acyltransferase. Chain: a, b, c. Synonym: lpxd. Engineered: yes

Source:

Chlamydia trachomatis. Organism_taxid: 813. Variant: serovar b. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.209 R-free: 0.256

Authors:

L.Buetow,T.K.Smith,A.Dawson,S.Fyffe,W.N.Hunter

Key ref:

L.Buetow et al. (2007). Structure and reactivity of LpxD, the N-acyltransferase of lipid A biosynthesis. Proc Natl Acad Sci U S A, 104, 4321-4326. PubMed id: 17360522 DOI: 10.1073/pnas.0606356104

Date:

30-May-06 Release date: 20-Feb-07

Protein chains

P0CD76  (LPXD_CHLTR) -  UDP-3-O-acylglucosamine N-acyltransferase from Chlamydia trachomatis serovar D (strain ATCC VR-885 / DSM 19411 / UW-3/Cx)

Seq: 354 a.a.

Struc: 346 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.1.191 - UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase.
• Reaction: a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + a (3R)-hydroxyacyl- [ACP] = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + holo- [ACP] + H⁺

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

Added reference

DOI no: 10.1073/pnas.0606356104

Proc Natl Acad Sci U S A 104:4321-4326 (2007)

PubMed id: 17360522

Structure and reactivity of LpxD, the N-acyltransferase of lipid A biosynthesis.

L.Buetow, T.K.Smith, A.Dawson, S.Fyffe, W.N.Hunter.

ABSTRACT

The external layer of the Gram-negative bacterial outer membrane is primarily composed of a protective, selectively permeable LPS. The biosynthesis of LPS relies on UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD), which transfers 3-hydroxy-arachidic acid from acyl carrier protein to the 2' amine of UDP-3-O-myristoyl glucosamine in Chlamydia trachomatis. Our crystallographic study reveals that LpxD is a homotrimer, each subunit of which is constructed from a novel combination of an N-terminal uridine-binding domain, a core lipid-binding domain, and a C-terminal helical extension. Highly conserved residues dominate nucleotide binding. Phe-43 and Tyr-49 form pi-stacking interactions with uracil, and Asn-46 and His-284 form hydrogen bonds with the phosphate groups. These interactions place the glucosamine moiety at the catalytic center formed by two adjacent subunits. Here His-247 and His-284 contribute to a mechanism involving nucleophilic attack by the amine of one substrate on the carbonyl carbon of an acyl carrier protein thioester conjugate. Serendipitously, our study reveals a fatty acid (FA) binding groove near the catalytic center. MS elucidated the presence of a FA mixture binding to LpxD, with palmitic acid the most prevalent. The placement of UDP-N-acetylglucosamine and the FA provides details of N-acyltransferase ligand interactions and allows for a description of structure and reactivity at an early stage of LPS assembly.

Selected figure(s)

Figure 2.
Fig. 2. Structure of LpxD. (A) Ribbon diagram of a subunit. The UBD is yellow, the LBD is blue, loops are magenta, and the HE is red. Selected elements of secondary structure are labeled, and the coils are numbered. (B) The trimer. The view is parallel to the noncrystallographic symmetry threefold axis. Subunits are colored gray, wheat, and slate, and the domains of the gray subunit are labeled. UDP-GlcNAc (complex II) is represented by spheres, and palmitic acid is represented by sticks. The atoms of the ligands are colored as follows: C, green; N, blue; O, red; P, yellow. (C) Orthogonal view of the trimer. (D) Primary and secondary structure. -strands are depicted by arrows, and -helices are depicted by cylinders. Colors are as described in A. Disordered residues at the C terminus are marked by dots. Highly conserved residues (>60% identity in 85 sequences) are highlighted in gray, and strictly conserved residues (100% identity) are in black. Green stars and circles indicate residues that interact with UDP-GlcNAc and palmitic acid, respectively. Salmon boxes represent sites of conditionally lethal point mutations in E. coli and S. typhimurium LpxD.

Figure 4.
Fig. 4. LpxD–FA complex. (A) Identification of bound FA. GC-MS analysis, chain length, and saturation states are indicated, and the key shows the relative percentages. (B) Surface view of conserved residues with ligands depicted as sticks. Palmitic acid is colored cyan, and UDP-GlcNAc is colored according to atom type: C, white; N, blue; O, red. Conserved residues are colored by type; basic residues are blue with the exception of His-247 and His-284, which are colored green. Acidic residues are red, aromatic residues are salmon, glycine residues are yellow, polar residues (Asn, Gln, Ser, Thr, and Cys) are slate blue, and aliphatic residues (Ala, Ile, Val, Leu, Met, and Pro) are magenta. Colored residues that form part of the FA and UDP-GlcNAc binding pockets include Gly-262, Gly-280, Gly-265, Ala-246, Ile-263, Ala-264, Asp-240, and Gln-244.

Figures were selected by the author.