PDBsum entry 1yhc

Hydrolase

PDB id

1yhc

Loading ...

Contents

			Protein chains

					266 a.a. *

			Ligands

					CAC ×2


					SO4 ×2


					PAM ×2


					GOL

			Metals

					_ZN ×5


					_CL ×3

			Waters ×319

* Residue conservation analysis

PDB id:

1yhc

Links

Name:

Hydrolase

Title:

Crystal structure of aquifex aeolicus lpxc deacetylase complexed with cacodylate

Structure:

Udp-3-o-[3-hydroxymyristoyl] n-acetylglucosamine deacetylase. Chain: a, b. Synonym: udp-3-o-acyl-glcnac deacetylase. Engineered: yes. Mutation: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: lpxc, enva. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å

R-factor:

0.180

R-free:

0.210

Authors:

M.Hernick,H.A.Gennadios,D.A.Whittington,K.M.Rusche,D.W.Christianson, C.A.Fierke

Key ref:

M.Hernick et al. (2005). UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism. J Biol Chem, 280, 16969-16978. PubMed id: 15705580 DOI: 10.1074/jbc.M413560200

Date:

07-Jan-05

Release date:

15-Feb-05

PROCHECK

	Headers

	References

Protein chains

O67648 (LPXC_AQUAE) - UDP-3-O-acyl-N-acetylglucosamine deacetylase from Aquifex aeolicus (strain VF5)

Seq: Struc:					282 a.a. 266 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.3.5.1.108 - UDP-3-O-acyl-N-acetylglucosamine deacetylase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate

UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine

H2O

UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine

acetate
Bound ligand (Het Group name = GOL)
matches with 42.86% similarity

Cofactor:

Zn(2+)

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

Key reference

DOI no: 10.1074/jbc.M413560200	J Biol Chem 280:16969-16978 (2005)
PubMed id: 15705580

UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism.
M.Hernick, H.A.Gennadios, D.A.Whittington, K.M.Rusche, D.W.Christianson, C.A.Fierke.

ABSTRACT

UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a zinc-dependent enzyme that catalyzes the deacetylation of UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine to form UDP-3-O-(R-hydroxymyristoyl)glucosamine and acetate. The structural similarity of the active site of LpxC to metalloproteases led to the proposal that LpxC functions via a metalloprotease-like mechanism. The pH dependence of k(cat)/Km catalyzed by Escherichia coli and Aquifex aeolicus LpxC displayed a bell-shaped curve (EcLpxC yields apparent pKa values of 6.4+/-0.1 and 9.1+/-0.1), demonstrating that at least two ionizations are important for maximal activity. Metal substitution and mutagenesis experiments suggest that the basic limb of the pH profile is because of deprotonation of a zinc-coordinated group such as the zinc-water molecule, whereas the acidic limb of the pH profile is caused by protonation of either Glu78 or His265. Furthermore, the magnitude of the activity decreases and synergy observed for the active site mutants suggest that Glu78 and His265 act as a general acid-base catalyst pair. Crystal structures of LpxC complexed with cacodylate or palmitate demonstrate that both Glu78 and His265 hydrogen-bond with the same oxygen atom of the tetrahedral intermediate and the product carboxylate. These structural features suggest that LpxC catalyzes deacetylation by using Glu78 and His265 as a general acid-base pair and the zinc-bound water as a nucleophile.

Selected figure(s)



	Figure 2. FIG. 2. a, structure of zinc-inhibited LpxC (Protein Data Bank accession code 1P42 [PDB] ) (15); A, catalytic zinc ion; B, inhibitory zinc ion. b, metal coordination interactions in the binuclear zinc cluster of zinc-inhibited LpxC.		Figure 3. FIG. 3. The proposed mechanisms for LpxC using either a single bifunctional GABC (A) or a GABC pair (B).

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21167751

C.J.Lee, X.Liang, X.Chen, D.Zeng, S.H.Joo, H.S.Chung, A.W.Barb, S.M.Swanson, R.A.Nicholas, Y.Li, E.J.Toone, C.R.Raetz, and P.Zhou (2011).
Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design.

Chem Biol, 18, 38-47.

PDB codes:

3p3c 3p3e 3p3g

20136146

M.Hernick, S.G.Gattis, J.E.Penner-Hahn, and C.A.Fierke (2010).
Activation of Escherichia coli UDP-3-O-[(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase by Fe2+ yields a more efficient enzyme with altered ligand affinity.

Biochemistry, 49, 2246-2255.

19256534

A.W.Barb, T.M.Leavy, L.I.Robins, Z.Guan, D.A.Six, P.Zhou, M.J.Hangauer, C.R.Bertozzi, and C.R.Raetz (2009).
Uridine-based inhibitors as new leads for antibiotics targeting Escherichia coli LpxC.

Biochemistry, 48, 3068-3077.

18761443

A.S.Lipton, R.W.Heck, M.Hernick, C.A.Fierke, and P.D.Ellis (2008).
Residue ionization in LpxC directly observed by 67Zn NMR spectroscopy.

J Am Chem Soc, 130, 12671-12679.

18289052

A.W.Barb, and P.Zhou (2008).
Mechanism and inhibition of LpxC: an essential zinc-dependent deacetylase of bacterial lipid A synthesis.

Curr Pharm Biotechnol, 9, 9.

18287278

I.Mochalkin, J.D.Knafels, and S.Lightle (2008).
Crystal structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor.

Protein Sci, 17, 450-457.

PDB code:

2ves

17335290

A.W.Barb, A.L.McClerren, K.Snehelatha, C.M.Reynolds, P.Zhou, and C.R.Raetz (2007).
Inhibition of lipid A biosynthesis as the primary mechanism of CHIR-090 antibiotic activity in Escherichia coli.

Biochemistry, 46, 3793-3802.

18025458

A.W.Barb, L.Jiang, C.R.Raetz, and P.Zhou (2007).
Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: Time-dependent inhibition and specificity in ligand binding.

Proc Natl Acad Sci U S A, 104, 18433-18438.

PDB code:

2jt2

17362200

C.R.Raetz, C.M.Reynolds, M.S.Trent, and R.E.Bishop (2007).
Lipid A modification systems in gram-negative bacteria.

Annu Rev Biochem, 76, 295-329.

16800620

H.A.Gennadios, D.A.Whittington, X.Li, C.A.Fierke, and D.W.Christianson (2006).
Mechanistic inferences from the binding of ligands to LpxC, a metal-dependent deacetylase.

Biochemistry, 45, 7940-7948.

PDB codes:

2go3 2go4

17176043

H.A.Gennadios, and D.W.Christianson (2006).
Binding of uridine 5'-diphosphate in the "basic patch" of the zinc deacetylase LpxC and implications for substrate binding.

Biochemistry, 45, 15216-15223.

PDB codes:

2ier 2ies

17077484

L.Buetow, A.Dawson, and W.N.Hunter (2006).
The nucleotide-binding site of Aquifex aeolicus LpxC.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1082-1086.

PDB code:

2j65

16342948

A.L.McClerren, S.Endsley, J.L.Bowman, N.H.Andersen, Z.Guan, J.Rudolph, and C.R.Raetz (2005).
A slow, tight-binding inhibitor of the zinc-dependent deacetylase LpxC of lipid A biosynthesis with antibiotic activity comparable to ciprofloxacin.

Biochemistry, 44, 16574-16583.

16141327

L.Di Costanzo, G.Sabio, A.Mora, P.C.Rodriguez, A.C.Ochoa, F.Centeno, and D.W.Christianson (2005).
Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response.

Proc Natl Acad Sci U S A, 102, 13058-13063.

PDB codes:

1wva 2aeb

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.