3T2P

E. coli (lacZ) beta-galactosidase (S796D) in complex with IPTG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Ser-796 of Beta-Galactosidase (E. coli) Plays a Key Role in Maintaining an Optimum Balance between the Opened and Closed Conformations of the Catalytically Important Active Site Loop

Jancewicz, L.J.Wheatley, R.W.Sutendra, G.Lee, M.Fraser, M.E.Huber, R.E.

(2012) Arch Biochem Biophys 517: 111-122

  • DOI: https://doi.org/10.1016/j.abb.2011.11.017
  • Primary Citation of Related Structures:  
    3SEP, 3T08, 3T09, 3T0A, 3T0B, 3T0D, 3T2O, 3T2P, 3T2Q

  • PubMed Abstract: 

    A loop (residues 794-803) at the active site of β-galactosidase (Escherichia coli) opens and closes during catalysis. The α and β carbons of Ser-796 form a hydrophobic connection to Phe-601 when the loop is closed while a connection via two H-bonds with the Ser hydroxyl occurs with the loop open. β-Galactosidases with substitutions for Ser-796 were investigated. Replacement by Ala strongly stabilizes the closed conformation because of greater hydrophobicity and loss of H-bonding ability while replacement with Thr stabilizes the open form through hydrophobic interactions with its methyl group. Upon substitution with Asp much of the defined loop structure is lost. The different open-closed equilibria cause differences in the stabilities of the enzyme·substrate and enzyme·transition state complexes and of the covalent intermediate that affect the activation thermodynamics. With Ala, large changes of both the galactosylation (k(2)) and degalactosylation (k(3)) rates occur. With Thr and Asp, the k(2) and k(3) were not changed as much but large ΔH(‡) and TΔS(‡) changes showed that the substitutions caused mechanistic changes. Overall, the hydrophobic and H-bonding properties of Ser-796 result in interactions strong enough to stabilize the open or closed conformations of the loop but weak enough to allow loop movement during the reaction.


  • Organizational Affiliation

    Division of Biochemistry, University of Calgary, Calgary, Alberta, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, B, C, D
1,052Escherichia coli K-12Mutation(s): 1 
Gene Names: b0344JW0335lacZ
EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12))
Explore P00722 
Go to UniProtKB:  P00722
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00722
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IPT
Query on IPT

Download Ideal Coordinates CCD File 
E [auth A],
QB [auth D],
SA [auth C],
Y [auth B]
1-methylethyl 1-thio-beta-D-galactopyranoside
C9 H18 O5 S
BPHPUYQFMNQIOC-NXRLNHOXSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AB [auth C]
AC [auth D]
BB [auth C]
BC [auth D]
CB [auth C]
AB [auth C],
AC [auth D],
BB [auth C],
BC [auth D],
CB [auth C],
CC [auth D],
DA [auth B],
DB [auth C],
DC [auth D],
EA [auth B],
EB [auth C],
EC [auth D],
FA [auth B],
FB [auth C],
FC [auth D],
GA [auth B],
GB [auth C],
GC [auth D],
HA [auth B],
HB [auth C],
HC [auth D],
IA [auth B],
IB [auth C],
IC [auth D],
JA [auth B],
JB [auth C],
JC [auth D],
K [auth A],
KA [auth B],
KB [auth C],
KC [auth D],
L [auth A],
LA [auth B],
LB [auth C],
M [auth A],
MA [auth B],
MB [auth C],
N [auth A],
NA [auth B],
NB [auth C],
O [auth A],
OA [auth B],
OB [auth C],
P [auth A],
PA [auth B],
PB [auth C],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
VB [auth D],
W [auth A],
WB [auth D],
X [auth A],
XB [auth D],
YA [auth C],
YB [auth D],
ZA [auth C],
ZB [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth B]
F [auth A]
G [auth A]
RB [auth D]
SB [auth D]
AA [auth B],
F [auth A],
G [auth A],
RB [auth D],
SB [auth D],
TA [auth C],
UA [auth C],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
H [auth A]
I [auth A]
J [auth A]
BA [auth B],
CA [auth B],
H [auth A],
I [auth A],
J [auth A],
TB [auth D],
UB [auth D],
VA [auth C],
WA [auth C],
XA [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
IPT BindingDB:  3T2P Ki: 7.60e+4 (nM) from 1 assay(s)
PDBBind:  3T2P Ki: 2.50e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.869α = 90
b = 166.171β = 90
c = 200.786γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Structure summary