7W8N

Microbial Hormone-sensitive lipase E53 wild type


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7CIP


Literature

Mechanism and Structural Insights Into a Novel Esterase, E53, Isolated From Erythrobacter longus .

Ding, Y.Nie, L.Yang, X.C.Li, Y.Huo, Y.Y.Li, Z.Gao, Y.Cui, H.L.Li, J.Xu, X.W.

(2021) Front Microbiol 12: 798194-798194

  • DOI: https://doi.org/10.3389/fmicb.2021.798194
  • Primary Citation of Related Structures:  
    7CI0, 7CIH, 7W8N

  • PubMed Abstract: 

    Esterases are a class of enzymes that split esters into an acid and an alcohol in a chemical reaction with water, having high potential in pharmaceutical, food and biofuel industrial applications. To advance the understanding of esterases, we have identified and characterized E53, an alkalophilic esterase from a marine bacterium Erythrobacter longus . The crystal structures of wild type E53 and three variants were solved successfully using the X-ray diffraction method. Phylogenetic analysis classified E53 as a member of the family IV esterase. The enzyme showed highest activity against p -nitrophenyl butyrate substrate at pH 8.5-9.5 and 40 ° C. Based on the structural feature, the catalytic pocket was defined as R1 (catalytic center), R2 (pocket entrance), and R3 (end area of pocket) regions. Nine variants were generated spanning R1-R3 and thorough functional studies were performed. Detailed structural analysis and the results obtained from the mutagenesis study revealed that mutations in the R1 region could regulate the catalytic reaction in both positive and negative directions; expanding the bottleneck in R2 region has improved the enzymatic activity; and R3 region was associated with the determination of the pH pattern of E53. N166A in R3 region showed reduced activity only under alkaline conditions, and structural analysis indicated the role of N166 in stabilizing the loop by forming a hydrogen bond with L193 and G233. In summary, the systematic studies on E53 performed in this work provide structural and functional insights into alkaliphilic esterases and further our knowledge of these enzymes.


  • Organizational Affiliation

    Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase
A, B, D
314Erythrobacter longusMutation(s): 0 
Gene Names: EH31_02760
UniProt
Find proteins for A0A074MDU6 (Erythrobacter longus)
Explore A0A074MDU6 
Go to UniProtKB:  A0A074MDU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A074MDU6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase314Erythrobacter longusMutation(s): 0 
Gene Names: EH31_02760
UniProt
Find proteins for A0A074MDU6 (Erythrobacter longus)
Explore A0A074MDU6 
Go to UniProtKB:  A0A074MDU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A074MDU6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D8F (Subject of Investigation/LOI)
Query on D8F

Download Ideal Coordinates CCD File 
MB [auth C],
NC [auth D],
T [auth A],
UA [auth B]
(4-nitrophenyl) hexanoate
C12 H15 N O4
OLRXUEYZKCCEKK-UHFFFAOYSA-N
NPO (Subject of Investigation/LOI)
Query on NPO

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LC [auth D],
RA [auth B],
SA [auth B]
P-NITROPHENOL
C6 H5 N O3
BTJIUGUIPKRLHP-UHFFFAOYSA-N
6NA (Subject of Investigation/LOI)
Query on 6NA

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CC [auth D],
FB [auth C],
G [auth A],
IC [auth D],
U [auth A]
HEXANOIC ACID
C6 H12 O2
FUZZWVXGSFPDMH-UHFFFAOYSA-N
SO4
Query on SO4

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W [auth A],
X [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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AC [auth D]
E [auth A]
EB [auth C]
IB [auth C]
JB [auth C]
AC [auth D],
E [auth A],
EB [auth C],
IB [auth C],
JB [auth C],
LB [auth C],
QA [auth B],
SB [auth D],
XA [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BUA
Query on BUA

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MA [auth B]butanoic acid
C4 H8 O2
FERIUCNNQQJTOY-UHFFFAOYSA-N
DIO
Query on DIO

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BA [auth B]1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
DMS
Query on DMS

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DC [auth D]
IA [auth B]
J [auth A]
JA [auth B]
K [auth A]
DC [auth D],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
NA [auth B],
OA [auth B],
OB [auth C],
R [auth A],
RB [auth D],
S [auth A],
TA [auth B],
ZB [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

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AA [auth B]
AB [auth C]
BB [auth C]
CA [auth B]
DA [auth B]
AA [auth B],
AB [auth C],
BB [auth C],
CA [auth B],
DA [auth B],
EC [auth D],
F [auth A],
FA [auth B],
H [auth A],
HB [auth C],
I [auth A],
KB [auth C],
MC [auth D],
NB [auth C],
P [auth A],
TB [auth D],
VA [auth B],
VB [auth D],
WA [auth C],
WB [auth D],
XB [auth D],
Y [auth B],
YA [auth C],
Z [auth B],
ZA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CCN
Query on CCN

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BC [auth D]
CB [auth C]
DB [auth C]
EA [auth B]
FC [auth D]
BC [auth D],
CB [auth C],
DB [auth C],
EA [auth B],
FC [auth D],
GA [auth B],
GB [auth C],
GC [auth D],
HA [auth B],
HC [auth D],
JC [auth D],
KA [auth B],
KC [auth D],
L [auth A],
LA [auth B],
M [auth A],
N [auth A],
O [auth A],
PA [auth B],
Q [auth A],
QB [auth C],
UB [auth D],
V [auth A],
YB [auth D]
ACETONITRILE
C2 H3 N
WEVYAHXRMPXWCK-UHFFFAOYSA-N
NA
Query on NA

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PB [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.576α = 90
b = 129.838β = 90
c = 221.079γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata scaling
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31770004

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Derived calculations
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description