PDBsum entry: 1ku0

Hydrolase

PDB id: 1ku0

Contents

Protein chains

388 a.a. *

Metals

_CA ×2

_ZN ×2

Waters ×257

* Residue conservation analysis

PDB id:

1ku0

Name:

Hydrolase

Title:

Structure of the bacillus stearothermophilus l1 lipase

Structure:

L1 lipase. Chain: a, b. Fragment: residues 30-417(seq db number). Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.185 R-free: 0.218

Authors:

S.-T.Jeong,H.-K.Kim,S.-J.Kim,S.-W.Chi,J.-G.Pan,T.-K.Oh,S.- E.Ryu

Key ref:

S.T.Jeong et al. (2002). Novel zinc-binding center and a temperature switch in the Bacillus stearothermophilus L1 lipase. J Biol Chem, 277, 17041-17047. PubMed id: 11859083 DOI: 10.1074/jbc.M200640200

Date:

18-Jan-02 Release date: 21-Aug-02

Protein chains

O66015  (O66015_GEOSE) -  Lipase

Seq: 417 a.a.

Struc: 388 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.1.3 - Triacylglycerol lipase.
• Reaction: Triacylglycerol + H₂O = diacylglycerol + a carboxylate

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: hydrolase activity (2 terms)

reference

DOI no: 10.1074/jbc.M200640200

J Biol Chem 277:17041-17047 (2002)

PubMed id: 11859083

Novel zinc-binding center and a temperature switch in the Bacillus stearothermophilus L1 lipase.

S.T.Jeong, H.K.Kim, S.J.Kim, S.W.Chi, J.G.Pan, T.K.Oh, S.E.Ryu.

ABSTRACT

The bacterial thermoalkalophilic lipases optimally hydrolyze saturated fatty acids at elevated temperatures. They also have significant sequence homology with staphylococcal lipases, and both the thermoalkalophilic and staphylococcal lipases are grouped as the lipase family I.5. We report here the first crystal structure of the lipase family I.5, the structure of a thermoalkalophilic lipase from Bacillus stearothermophilus L1 (L1 lipase) determined at 2.0-A resolution. The structure is in a closed conformation, and the active site is buried under a long lid helix. Unexpectedly, the structure exhibits a zinc-binding site in an extra domain that accounts for the larger molecular size of the family I.5 enzymes in comparison to other microbial lipases. The zinc-coordinated extra domain makes tight interactions with the loop extended from the C terminus of the lid helix, suggesting that the activation of the family I.5 lipases may be regulated by the strength of the interactions. The unusually long lid helix makes strong hydrophobic interactions with its neighbors. The structural information together with previous biochemical observations indicate that the temperature-mediated lid opening is triggered by the thermal dissociation of the hydrophobic interactions.

Selected figure(s)

Figure 3.
Fig. 3. Side-chain packing of the catalytic triad region. Characteristic substitutions in L1 lipase (Phe-16, Ile-319, Thr-269, and Met-325) near catalytic triad residues are presented as superposed with corresponding residues of C. viscosum (Leu-17, Leu-265, Gly-211, and Ser-271). Side chains of L1 lipase (purple) and C. viscosum lipase (cyan) are drawn in a ball-and-stick representation. Only the C trace of L1 lipase is presented because the two enzymes exhibits a good C trace alignment in the region. Side-chain conformations of catalytic triad residues (Ser-113, His-358, and Asp-317) also are well aligned between the two structures, and only those of L1 lipase are presented in the figure.

Figure 5.
Fig. 5. The lid helix. a, a comparison of the lid helix. The lid helices and adjustable loops flanking the lid helices of L1 lipase (yellow) and C. viscosum lipase (blue) are presented as superposed by using the orientation matrix obtained from the alignment of Fig. 1b. Residues 174-221 and residues 130-155 are drawn for L1 lipase and C. viscosum lipase, respectively. The C-terminal region of the L1 lipase lid helix (residues 193-204), which has alternative conformations, is indicated with a different color (pink). b, the hydrophobic interactions of the L1 lipase lid helix. Side chains of residues involved in the hydrophobic interactions of the L1 lipase lid helix with neighbors were drawn on the C trace diagram of the L1 lipase structure. Residues in the lid helix and neighbors are colored cyan (labeled blue) and pink (labeled red), respectively. The C trace of the lid helix is colored yellow to distinguish the helix from other regions of the protein.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 17041-17047) copyright 2002.

Figures were selected by an automated process.