2QUB

Crystal structure of extracellular lipase LipA from Serratia marcescens

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

A calcium-gated lid and a large beta-roll sandwich are revealed by the crystal structure of extracellular lipase from Serratia marcescens.

Meier, R., Drepper, T., Svensson, V., Jaeger, K.E., Baumann, U.

(2007) J Biol Chem 282: 31477-31483

  • DOI: 10.1074/jbc.M704942200
  • Primary Citation of Related Structures:  
    2QUA, 2QUB

  • PubMed Abstract: 

    • Lipase LipA from Serratia marcescens is a 613-amino acid enzyme belonging to family I.3 of lipolytic enzymes that has an important biotechnological application in the production of a chiral precursor for the coronary vasodilator diltiazem. Like other family I ...

    Lipase LipA from Serratia marcescens is a 613-amino acid enzyme belonging to family I.3 of lipolytic enzymes that has an important biotechnological application in the production of a chiral precursor for the coronary vasodilator diltiazem. Like other family I.3 lipases, LipA is secreted by Gram-negative bacteria via a type I secretion system and possesses 13 copies of a calcium binding tandem repeat motif, GGXGXDXUX (U, hydrophobic amino acids), in the C-terminal part of the polypeptide chain. The 1.8-A crystal structure of LipA reveals a close relation to eukaryotic lipases, whereas family I.1 and I.2 enzymes appear to be more distantly related. Interestingly, the structure shows for the N-terminal lipase domain a variation on the canonical alpha/beta hydrolase fold in an open conformation, where the putative lid helix is anchored by a Ca(2+) ion essential for activity. Another novel feature observed in this lipase structure is the presence of a helical hairpin additional to the putative lid helix that exposes a hydrophobic surface to the aqueous medium and might function as an additional lid. The tandem repeats form two separated parallel beta-roll domains that pack tightly against each other. Variations of the consensus sequence of the tandem repeats within the second beta-roll result in an asymmetric Ca(2+) binding on only one side of the roll. The analysis of the properties of the beta-roll domains suggests an intramolecular chaperone function.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University Bern Freiestrasse 3, CH-3012 Bern, Switzerland.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Extracellular lipase615Serratia marcescensMutation(s): 0 
Gene Names: lipA
EC: 3.1.1.3
UniProt
Find proteins for Q59933 (Serratia marcescens)
Explore Q59933 
Go to UniProtKB:  Q59933
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59933
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
AA [auth E],
AB [auth K],
BA [auth E],
BB [auth K],
CA [auth E],
AA [auth E],
AB [auth K],
BA [auth E],
BB [auth K],
CA [auth E],
DA [auth E],
EA [auth G],
FA [auth G],
G [auth A],
GA [auth G],
H [auth A],
HA [auth G],
I [auth A],
IA [auth G],
J [auth A],
JA [auth G],
K [auth A],
KA [auth G],
L [auth A],
LA [auth G],
M [auth A],
MA [auth I],
N [auth A],
NA [auth I],
O [auth C],
OA [auth I],
P [auth C],
PA [auth I],
Q [auth C],
QA [auth I],
R [auth C],
RA [auth I],
S [auth C],
SA [auth I],
T [auth C],
TA [auth I],
U [auth C],
UA [auth K],
V [auth C],
VA [auth K],
W [auth E],
WA [auth K],
X [auth E],
XA [auth K],
Y [auth E],
YA [auth K],
Z [auth E],
ZA [auth K]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.401α = 90
b = 202.401β = 90
c = 317.731γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-08-04 
  • Released Date: 2007-08-28 
    • Deposition Author(s): Meier, R., Baumann, U.

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance